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98 results on '"LabeX NUMEV '

1. Experimental evidence for long-distance electrodynamic intermolecular forces

Author: Lechelon, Mathias, Meriguet, Yoann, Gori, Matteo, Ruffenach, Sandra, Nardecchia, Ilaria, Floriani, Elena, Coquillat, Dominique, Teppe, Frédéric, Mailfert, Sébastien, Marguet, Didier, Ferrier, Pierre, Varani, Luca, Sturgis, James, Torres, Jeremie, Pettini, Marco, Centre de Physique Théorique - UMR 7332 (CPT), Aix Marseille Université (AMU)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), CPT - E7 Systèmes dynamiques : théories et applications, Aix Marseille Université (AMU)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Centre d'Immunologie de Marseille - Luminy (CIML), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU), Institut d’Electronique et des Systèmes (IES), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Charles Coulomb (L2C), Howard University, Modélisation et Spectroscopie THz (MOST), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'ingénierie des systèmes macromoléculaires (LISM), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Aix Marseille Université (AMU), Excellence Initiative of Aix-Marseille University, European Commission, ANR, CNRS, Excellence Initiative of Aix-Marseille University - A*MIDEX, a French 'Investissements d'Avenir' programme., Projects SIDERANT and NEBULA financed by the french CNRS, by the Occitanie Region and by Montpellier University through its TOP platform and by the LabEx NUMEV (ANR-10-LABX-0020) within the I-Site MUSE, ANR-10-LABX-0020,NUMEV,Digital and Hardware Solutions and Modeling for the Environement and Life Sciences(2010), ANR-10-INBS-0004,France-BioImaging,Développment d'une infrastructure française distribuée coordonnée(2010), European Project: 765426,TeraApps, European Project: 964203,FET-Open LINkS, Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Excellence Initiative of Aix-Marseille University - A*MIDEX, a French 'Investissements d'Avenir' programme., Projects SIDERANT and NEBULA financed by the french CNRS, by the Occitanie Region and by Montpellier University through its TOP platform and by the LabEx NUMEV (ANR-10-LABX-0020) within the I-Site MUSE, This project has received funding from the European Union’s Horizon 2020 Research and Innovation Programme under grant agreement no. 964203 (FET-Open LINkS project)., Pettini, Marco, Laboratoires d'excellence - Digital and Hardware Solutions and Modeling for the Environement and Life Sciences - - NUMEV2010 - ANR-10-LABX-0020 - LABX - VALID, and Développment d'une infrastructure française distribuée coordonnée - - France-BioImaging2010 - ANR-10-INBS-0004 - INBS - VALID
Subjects: Horizon 2020, Multidisciplinary, [PHYS.PHYS.PHYS-BIO-PH] Physics [physics]/Physics [physics]/Biological Physics [physics.bio-ph], Electrodynamical-Interactions, [PHYS.PHYS.PHYS-BIO-PH]Physics [physics]/Physics [physics]/Biological Physics [physics.bio-ph], FOS: Physical sciences, Biophysics (molecular), Quantum Biology, TeraHertz THz, Condensed Matter - Soft Condensed Matter, Biological Physics (physics.bio-ph), collective molecular oscillations, Terahertz spectroscopy, biophysics, Fluorescence Correlation Spectroscopy, Soft Condensed Matter (cond-mat.soft), Physical sciences — Condensed Matter Physics, European Union, Physics - Biological Physics, Physics - Atomic and Molecular Clusters, Electrodynamic intermolecular interactions, Atomic and Molecular Clusters (physics.atm-clus), Spectroscopy
Abstract: Both classical and quantum electrodynamics predict the existence of dipole-dipole long-range electrodynamic intermolecular forces; however, these have never been hitherto experimentally observed. The discovery of completely new and unanticipated forces acting between biomolecules could have considerable impact on our understanding of the dynamics and functioning of the molecular machines at work in living organisms. Here, using two independent experiments, on the basis of different physical effects detected by fluorescence correlation spectroscopy and terahertz spectroscopy, respectively, we demonstrate experimentally the activation of resonant electrodynamic intermolecular forces. This is an unprecedented experimental proof of principle of a physical phenomenon that, having been observed for biomacromolecules and with long-range action (up to 1000 Angstroms), could be of importance for biology. In addition to thermal fluctuations that drive molecular motion randomly, these resonant (and thus selective) electrodynamic forces may contribute to molecular encounters in the crowded cellular space., 40 pages, 8 figures, Supplementary material for this article (additional data, theory and 4 movies) is available at https://www.science.org/doi/10.1126/sciadv.abl5855#con1
Published: 2022

2. Second-order cone optimization of the gradostat

Author: Alain Rapaport, Josh A. Taylor, Department of Electrical and Computer Engineering [University of Toronto] (ECE), University of Toronto, Mathématiques, Informatique et STatistique pour l'Environnement et l'Agronomie (MISTEA), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Labex NUMEV incorporated into the I-Site MUSE, ANR-10-LABX-0020,NUMEV,Digital and Hardware Solutions and Modeling for the Environement and Life Sciences(2010), Natural Sciences and Engineering Research Council of Canada, French LabEx NUMEV (Project ANR-10 LABX-20), incorporated into the I-Site MUSE, and ANR-10-LABX-0020,NUMEV,ANR-10 LABX-20(2010)
Subjects: 020209 energy, General Chemical Engineering, 02 engineering and technology, Gradostat, 020401 chemical engineering, Simple (abstract algebra), second-order cone programming, FOS: Mathematics, 0202 electrical engineering, electronic engineering, information engineering, biogas, Applied mathematics, Growth rate, 0204 chemical engineering, Diffusion (business), Mathematics - Optimization and Control, Mathematics, Steady state, convex relaxation, 6. Clean water, Computer Science Applications, Constraint (information theory), wastewater treatment, Cone (topology), Optimization and Control (math.OC), Outflow, Relaxation (approximation), [MATH.MATH-OC]Mathematics [math]/Optimization and Control [math.OC]
Abstract: International audience; The gradostat consists of multiple chemostats interconnected by mass flows and diffusion. It has been used to model biochemical systems such as wastewater treatment networks and microbial activity in soil. In this paper we maximize the production of biogas in a gradostat at steady state. The physical decision variables are the water, substrate, and biomass entering each tank and the flows through the interconnecting pipes. Our main technical focus is the nonconvex constraint describing microbial growth. We formulate a relaxation and prove that it is exact when the gradostat is outflow connected, its system matrix is irreducible, and the growth rate satisfies a simple condition. The relaxation has second-order cone representations for the Monod and Contois growth rates. We extend the steady state models to the case of multiple time periods by replacing the derivatives with numerical approximations instead of setting them to zero. The resulting optimizations are second-order cone programs, which can be solved at large scales using standard industrial software.
Published: 2021

3. About frame estimation of growth functions and robust prediction in bioprocess modeling

Author: Emna Krichen, Alain Rapaport, Eric Fouilland, MARine Biodiversity Exploitation and Conservation (UMR MARBEC), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut de Recherche pour le Développement (IRD), Mathématiques, Informatique et STatistique pour l'Environnement et l'Agronomie (MISTEA), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), ADEME, Labex Numev, ANR-14-CE04-0011,Phycover,Durabilité des productions microalgales par recyclage du phosphore et de l'azote des eaux résiduaires : vers la station d'épuration du futur(2014), ANR-10-LABX-0020,NUMEV,Digital and Hardware Solutions and Modeling for the Environement and Life Sciences(2010), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), LabeX NUMEV & ADEME, Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), ANR: 10-LABX-0020,NUMEV,Digital and Hardware Solutions and Modeling for the Environement and Life Sciences(2010), Rapaport, Alain, and Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro
Subjects: 0209 industrial biotechnology, Mathematical optimization, Computer science, frame, [SDV]Life Sciences [q-bio], [MATH.MATH-DS]Mathematics [math]/Dynamical Systems [math.DS], [MATH.MATH-DS] Mathematics [math]/Dynamical Systems [math.DS], growth functions, Biotechnologies, Functional estimation, Least square, 02 engineering and technology, Systèmes dynamiques, functional estimation, Industrial and Manufacturing Engineering, 020901 industrial engineering & automation, 020401 chemical engineering, intervals, Statistiques (Mathématiques), 0204 chemical engineering, Bioprocess, [INFO.INFO-BT]Computer Science [cs]/Biotechnology, modélisation, biomathématique, robust prediction, estimation, Experimental data, Continuous mode, Interval observers, Growth functions, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, Dynamical Systems, contrôle de bioprocédé, Computer Science Applications, [STAT]Statistics [stat], mathématiques appliquées, least square, [INFO.INFO-BT] Computer Science [cs]/Biotechnology, Control and Systems Engineering, Modeling and Simulation, interval observers, [INFO.INFO-MO] Computer Science [cs]/Modeling and Simulation
Abstract: International audience; We address the problem of determining functional framing from experimental data points in view of robust time-varying predictions, which is of crucial importance in bioprocess monitoring. We propose a method that provides guaranteed functional bounds, instead of sets of parameters values for growth functions such as the classical Monod or Haldane functions commonly used in bioprocess modeling. We illustrate the applicability of the method with bioreactor simulations in batch and continuous mode, as well as on real data. We also present two extensions of the method adding flexibility in its application, and discuss its efficiency in providing guaranteed state estimations.
Published: 2020

4. Optimal periodic control for scalar dynamics under integral constraint on the input

Author: Fatima Zahra Tani, Alain Rapaport, Térence Bayen, Institut Montpelliérain Alexander Grothendieck (IMAG), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Mathématiques, Informatique et STatistique pour l'Environnement et l'Agronomie (MISTEA), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA), LabEx NUMEV incorporated into the I-Site MUSE (AAP2017- 2-08), French-Algerian AVERROES program of PhD 'bourses d'excellence', ANR: 16-CE04-0003,THERMOMIC,Un cadre thermodynamique pour la modélisation de la croissance et des dynamiques microbiennes, Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Labex NUMEV and I-Site MUSE (AAP2017- 2-08), Institut Montpelliérain Alexander Grothendieck ( IMAG ), Université de Montpellier ( UM ) -Centre National de la Recherche Scientifique ( CNRS ), Mathématiques, Informatique et STatistique pour l'Environnement et l'Agronomie ( MISTEA ), Institut National de la Recherche Agronomique ( INRA ) -Institut national d’études supérieures agronomiques de Montpellier ( Montpellier SupAgro ), ANR : 16-CE04-0003,THERMOMIC,Un cadre thermodynamique pour la modélisation de la croissance et des dynamiques microbiennes, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), EA2151 Laboratoire de Mathématiques d'Avignon (LMA), Avignon Université (AU), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), AVERROES program between Algeria and France, LabEx NUMEV incorporated into the I-Site MUSE : AAP2017-2-08, and ANR-16-CE04-0003,Thermomic,Un cadre thermodynamique pour la modélisation de la croissance et des dynamiques microbiennes(2016)
Subjects: Discrete mathematics, [ MATH ] Mathematics [math], [ MATH.MATH-OC ] Mathematics [math]/Optimization and Control [math.OC], 0209 industrial biotechnology, 021103 operations research, Control and Optimization, Periodic solutions, Optimal Control, Applied Mathematics, Scalar (mathematics), 0211 other engineering and technologies, 02 engineering and technology, Optimal control, Pontryagin's minimum principle, Chemostat Model, 020901 industrial engineering & automation, ComputingMethodologies_DOCUMENTANDTEXTPROCESSING, Over-yielding, [MATH.MATH-OC]Mathematics [math]/Optimization and Control [math.OC], [MATH]Mathematics [math], Pontryagin Maximum Principle, Mathematics
Abstract: This paper studies a periodic optimal control problem governed by a one-dimensional system, linear with respect to the control \begin{document}$ u $\end{document} , under an integral constraint on \begin{document}$ u $\end{document} . We give conditions for which the value of the cost function at steady state with a constant control \begin{document}$ \bar u $\end{document} can be improved by considering periodic control \begin{document}$ u $\end{document} with average value equal to \begin{document}$ \bar u $\end{document} . This leads to the so-called "over-yielding" met in several applications. With the use of the Pontryagin Maximum Principle, we provide the optimal synthesis of periodic strategies under the integral constraint. The results are illustrated on a single population model in order to study the effect of periodic inputs on the utility of the stock of resource.
Published: 2018

5. Emplacements optimaux de rejets pour la recharge de réservoirs hydriques à l’aide d’eaux usées traitées - application au cas d’étude du lac de Jaunay

Author: Crespo Moya, Maria, Orsoni, Julien, Bortoli, Jérôme, Rapaport, Alain, Rousseau, Antoine, Jauzein, Vincent, Université de Montpellier (UM), Mathématiques, Informatique et STatistique pour l'Environnement et l'Agronomie (MISTEA), Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Vendée Eau, Littoral, Environment: MOdels and Numerics (LEMON), Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut Montpelliérain Alexander Grothendieck (IMAG), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Hydrosciences Montpellier (HSM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), SAUR - Direction de la Recherche et Développement, SAUR, Labex Numev, ANR-10-LABX-0020,NUMEV,Digital and Hardware Solutions and Modeling for the Environement and Life Sciences(2010), Mathématiques, Informatique et STatistique pour l'Environnement et l'Agronomie ( MISTEA ), Institut National de la Recherche Agronomique ( INRA ) -Institut national d’études supérieures agronomiques de Montpellier ( Montpellier SupAgro ), Université de Montpellier ( UM ), Littoral, Environnement : Méthodes et Outils Numériques ( LEMON ), Inria Sophia Antipolis - Méditerranée ( CRISAM ), Institut National de Recherche en Informatique et en Automatique ( Inria ) -Institut National de Recherche en Informatique et en Automatique ( Inria ), Labex NUMEV, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Littoral, Environnement : Méthodes et Outils Numériques (LEMON), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and ANR: 10-LABX-0020,NUMEV,Digital and Hardware Solutions and Modeling for the Environement and Life Sciences(2010)
Subjects: lac, [ MATH.MATH-OC ] Mathematics [math]/Optimization and Control [math.OC], modélisation informatique, water resources management, optimisation multiobjective, [SDE.IE]Environmental Sciences/Environmental Engineering, Mécanique des fluides, stratégie optimale, computational modelling, pollutant propagation, wastewater reuse, réutilisation des eaux usées traitées, gestion des ressources en eau, [ SDE.IE ] Environmental Sciences/Environmental Engineering, mathématiques appliquées, multi-objective optimization, [ SPI.FLUID ] Engineering Sciences [physics]/Reactive fluid environment, Optimization and Control, réutilisation des eaux usées, propagation de polluant, modélisation computationnelle, optimisation multi-objectif, Fluids mechanics, Optimisation et contrôle, [MATH.MATH-OC]Mathematics [math]/Optimization and Control [math.OC], eaux usées, modélisation
Abstract: In this work, we study optimal strategies of wastewater reuse for refilling a large hydric reservoir (such as lake, pond, lagoon…) which shows an alarming volume reduction due to the human water intake. To grasp the multiple issues to ascertain the appropriate location for the reused water discharge, computational modelling is particularly adapted for testing different conditions (physical, meteorological) and optimizing the system to achieve targets (maximum allowable concentration of pollutant for drinking water and recreational uses). We focus on modelling the distribution of a generic pollutant in the reservoir, which is expected to vary with time and space. The model assumes that the reservoir volume stays constant (because the flow rates at the refilling and removal points are considered to be quasi-identical), the density of the pollutant is smaller than that of the reservoir water (so that the pollutant remains at the top level of the water column) and its dynamics is influenced by two main effects: wind and water currents. The model accounts for the reservoir geometry, the operating conditions of the transfer pipes (input and output) and real data regarding chronicles of wind velocity and river flow. Then, we tackle a multi-optimization problem which aims to find optimal refilling locations which reduce the pollutant concentration at two strategic regions of the reservoir. A Pareto front is presented as a decision-tool to choose the optimal strategy according to different water quality criteria. The methodology has been applied in the case of Jaunay Lake, a water reservoir located on the French western coast., Dans ce travail, nous étudions des stratégies optimales de réutilisation d’eaux usées pour le remplissage d’un grand réservoir d’eau (lac, étang, lagune…), qui montre une réduction de volume alarmante due à la consommation humaine. Afin d’appréhender les multiples difficultés pour déterminer l'emplacement approprié du point de rejet, la modélisation computationnelle est particulièrement adaptée pour tester différentes conditions (physiques, météorologiques) et optimiser le système pour atteindre des cibles (concentration maximale du polluant pour de l'eau potable et des activités récréatives). Nous nous concentrons sur la modélisation de la distribution d'un polluant générique dans le réservoir qui varie en temps et en espace. Le modèle suppose que le volume du réservoir reste constant (en considérant que les débits aux points du rejet et de la prise d’eau sont quasiment identiques). La densité du polluant est supposée inférieure à celle de l'eau (donc le polluant reste à la surface de la colonne d’eau) et sa dynamique est influencée par deux effets principaux: les courants d’eau et le vent. Le modèle tient compte de la géométrie du réservoir, des conditions du pompage (en entrée et en sortie) et des données réelles concernant les chroniques du vent et du débit de la rivière. Ensuite, nous abordons un problème d’optimisation multi-objectifs qui vise à trouver des emplacements optimaux de recharge qui réduisent la concentration du polluant dans deux régions stratégiques du réservoir. Un front de Pareto est présenté comme un outil de décision qui permet de choisir la stratégie optimale en fonction des différents critères sur la qualité de l'eau. La méthodologie a été appliquée dans le cas du Lac de Jaunay, un réservoir d'eau situé sur la côte ouest française.
Published: 2018

6. JOURDAIN : Project of Indirect Potable Reuse (IPR) demonstrator in Vendée: Computational modelling as an enhancement tool

Author: Crespo Moya, Maria, Orsoni, Julien, Bortoli, Jérôme, Rapaport, Alain, Rousseau, Antoine, Mathématiques, Informatique et STatistique pour l'Environnement et l'Agronomie (MISTEA), Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Université de Montpellier (UM), Vendée Eau, Littoral, Environment: MOdels and Numerics (LEMON), Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut Montpelliérain Alexander Grothendieck (IMAG), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Hydrosciences Montpellier (HSM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Labex NUMEV, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Littoral, Environnement : Méthodes et Outils Numériques (LEMON), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA), and Labex Numev
Subjects: [SPI.FLUID]Engineering Sciences [physics]/Reactive fluid environment, [MATH.MATH-AP]Mathematics [math]/Analysis of PDEs [math.AP], [MATH.MATH-OC]Mathematics [math]/Optimization and Control [math.OC]
Abstract: International audience; VENDEE EAU, a non profit public body in charge of water supply on the French western coast (264 municipalities, 600,000 inhabitants), produces 40 million m3 of drinking water per year mainly from surface resources. In order to face an estimated water deficit during a hot year the proposed solution is the indirect reuse from a coastal WWTP (Sables d’Olonne) to complete the volume of a fresh water reservoir (Jaunay). On account of the absence of regulations and unprecedented cases of IPR in France, VENDEE EAU envisions the implementation of a 1:4-scale demonstrator during the 2018-2024 period including tertiary treatment unit, transfer pipe, discharge zone and an extensive analytical program. Towards the multiple approaches to ascertain the appropriate location for the Reuse discharge point in the reservoir and suitable operational set points and flow rate, computational modelling is particularly adapted for testing different conditions (physical, meteorological) and optimizing the system to achieve targets (maximum allowable concentration of pollutant for drinking water and recreational uses In this work, we have focused on modelling the distribution of a generic pollutant in the reservoir, which is expected to vary with time and depending on system and meteorological conditions. We shall present a first computational model assuming that flow rate at the discharge point compensates the removal flow rate (so that the volume of the reservoir stays constant) and that the pollutant dynamics is influenced by two main effects: wind and water currents (resulting from the pumping processes and the discharge of Jaunay River into the reservoir). The model accounts for the geometry of the reservoir, the operating conditions of the transfer pipes and real data regarding chronicles of wind velocity, river flow and pollutant characteristics. Then, we have performed an optimization of the refilling location to minimize the pollutant concentration at strategic locations (with data from July-September 2016). Other meteorological conditions (such as rain and evaporation) may have a significant impact on the evolution of the pollutant distribution and disallow the assumption of constant volume of the reservoir. Extensions for taking into account variable volume will be discussed. Part of this work has been developed by students of the Master in Mathematical Engineering at UCM (Madrid, Spain) within the XI UCM Modelling Week.
Published: 2017

7. The orientation of the stimulating bipolar probe modulates axono-cortical evoked potentials

Author: Schlosser-Perrin, Félix, Rossel, Olivier, Duffau, Hugues, Matsumoto, Riki, Mandonnet, Emmanuel, Bonnetblanc, François, CAMIN Team, INRIA, Montpellier, France (INRIA), Département de Neurochirurgie, Centre Hospitalier Universitaire de Montpellier Gui de Chauliac, Montpellier, France (CHU GC), Division of Neurology, Kobe University Graduate School of Medicine, Japan (KU), Service de neurochirurgie [AP-HP Hôpital Lariboisière], AP-HP Groupe Hospitalier Lariboisière, Research supported by French 'Association pour la Recherche sur le Cancer' (ARC-France, project n° ARCPGA12019110000940_1572), the LabEx NUMEV project (n°ANR- 10-LABX-0020) within the I-Site MUSE (ANR-16-IDEX-0006), and and INRIA through an associate team between France (FB) and Japan (RM). RM was supported by a Kobe University Strategic International Collaborative Research Grant (Type B Fostering Joint Research).
Subjects: [PHYS]Physics [physics], [SCCO]Cognitive science
Abstract: International audience
Published: 2023

8. 3-Shortest Superstring is 2-approximable by a greedy algorithm

Author: Cazaux, Bastien, Rivals, Eric, Institut de Biologie Computationnelle (IBC), Institut National de la Recherche Agronomique (INRA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Méthodes et Algorithmes pour la Bioinformatique (MAB), Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Défi MASTODONS SePhHaDe from CNRS Labex NUMev, LIRMM, Financement : Défi MASTODONS SePhHaDe from CNRS Labex NUMev, ANR-12-BS02-0008,Colib'read,Méthodes d'extraction d'information biologique dans les données HTS non assemblées(2012), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), and Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)
Subjects: assembly, Shortest Common Superstring Problem, stringology, greedy conjecture, [INFO.INFO-DS]Computer Science [cs]/Data Structures and Algorithms [cs.DS], [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Approximation algorithm, data compression
Abstract: submitted; A superstring of a set of words is a string that contains each input word as a sub-string. Given such a set, the Shortest Superstring Problem (SSP) asks for a super-string of minimum length. SSP is an important theoretical problem related to the Asymmetric Travelling Salesman Problem, and also has practical applications in data compression and in bioinformatics. Indeed, it models the question of assembling a genome from a set of sequencing reads. Unfortunately, SSP is known to be NP-hard even on a binary alphabet and also hard to approximate with respect to the superstring length or to the compression achieved by the superstring. Even the variant in which all words share the same length r, called r-SSP, is NP-hard whenever r > 2. Numerous involved approximation algorithms achieve approximation ratio above 2 for the superstring, but remain difficult to implement in practice. In contrast the greedy conjecture asked in 1988 whether a simple greedy agglomeration algorithm achieves ratio of 2 for SSP. Here, we present a novel approach to bound the superstring approximation ratio with the compression ratio, which leads to a first proof of the greedy conjecture for 3-SSP.
Published: 2014

9. Experimental evidence for long-distance electrodynamic intermolecular forces

Author: Lechelon, Mathias, Meriguet, Yoann, Gori, Matteo, Ruffenach, Sandra, Nardecchia, Ilaria, Floriani, Elena, Kudashova, Anastasiia, Coquillat, Dominique, Teppe, Frédéric, Mailfert, Sébastien, Marguet, Didier, Ferrier, Pierre, Varani, Luca, Sturgis, James, Torres, Jeremie, Pettini, Marco, Centre de Physique Théorique - UMR 7332 (CPT), Aix Marseille Université (AMU)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), CPT - E7 Systèmes dynamiques : théories et applications, Aix Marseille Université (AMU)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Centre d'Immunologie de Marseille - Luminy (CIML), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU), Institut d’Electronique et des Systèmes (IES), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Charles Coulomb (L2C), Howard University, Modélisation et Spectroscopie THz (MOST), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'ingénierie des systèmes macromoléculaires (LISM), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Aix Marseille Université (AMU), Excellence Initiative of Aix-Marseille University, European Commission, ANR, CNRS, Excellence Initiative of Aix-Marseille University - A*MIDEX, a French 'Investissements d'Avenir' programme., Projects SIDERANT and NEBULA financed by the french CNRS, by the Occitanie Region and by Montpellier University through its TOP platform and by the LabEx NUMEV (ANR-10-LABX-0020) within the I-Site MUSE, and Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: [PHYS]Physics [physics], collective molecular oscillations, Terahertz spectroscopy, [PHYS.PHYS.PHYS-BIO-PH]Physics [physics]/Physics [physics]/Biological Physics [physics.bio-ph], biophysics, Fluorescence Correlation Spectroscopy, Electrodynamic intermolecular interactions
Abstract: International audience; Both Classical and Quantum Electrodynamics predict the existence of dipole-dipole long-range electrodynamic intermolecular forces, however these have never been hitherto experimentally observed. The discovery of completely new and unanticipated forces acting between biomolecules could have considerable impact on our understanding of the dynamics and functioning of the molecular machines at work in living organisms. Here, using two independent approaches, we demonstrate experimentally for the first time the activation of resonant electrodynamic intermolecular forces. We characterize clustering transitions induced by these forces by fluorescence correlation spectroscopy when out-of-equilibrium conditions induce collective molecular oscillation observed by Terahertz (THz) spectroscopy. This is an unprecedented experimental \textit{proof of principle} of a physical phenomenon that, having been observed for bio-macromolecules and with a long-range of action (up to 1000 ${\mathring{A}}$), could be of importance for biology. Therefore, in addition to thermal fluctuations that drive molecular motion randomly, these resonant (and thus selective) electrodynamic forces may contribute to molecular encounters in the crowded cellular space. We anticipate our findings will provide a basis for future systematic deepening of physical aspects of the reported phenomena and for future systematic assessment of the relevance of electrodynamic forces in shaping the dynamics of biomolecular encounters and recognition in biology.
Published: 2021

10. Algorithms for probabilistic motif search: the case of dinucleotidic Position Weight Matrices (di-PWM)

Author: Mille, Marie, Méthodes et Algorithmes pour la Bioinformatique (MAB), Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Université de Montpellier, and Flagship project GEM from Labex NUMEV
Subjects: python, logiciel, [INFO.INFO-DS]Computer Science [cs]/Data Structures and Algorithms [cs.DS], motifs, PWM, recherche, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], indexation, bioinformatique, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], algorithme, di-PWM, génomique
Abstract: Chaque facteur de transcription se lie à diverses séquences d'ADN ressemblantes, mais pas identiques, entre elles. Cet ensemble de séquences cibles peut être représenté par un motif probabiliste tel qu'une Matrice Poids Position (Position Weight Matrix en anglais -- PWM). Une PWM comporte un nombre de colonnes égal à la longueur des motifs identifiés par des méthodes expérimentales, et un nombre de lignes égal à 4 (pour A, T, G ou C). Chaque colonne stocke la probabilité d'apparition de chacun des 4 nucléotides possibles pour chaque position des séquences cibles. Dans une PWM, les colonnes sont indépendantes les unes des autres : ce modèle ne peut transcrire entre positions voisines. Pour dépasser cette limitation, Kulakovskiy et al. ont proposé les dinucleotidic PWM, où chaque colonne stocke la probabilité de tous les di-nucléotides possibles (AA, AC, AG, etc.). Dans ce travail de Master, nous proposons différents algorithmes génériques pour rechercher les occurrences de di-PWM dans un texte qui représente une longue séquence d'ADN ou d'ARN. En particulier, nous proposons des accélérations pour une stratégie dite de fenêtre glissante, où l'on scanne le texte afin de trouver une fenêtre dont le score selon la matrice est supérieur à un seuil donnée. Ensuite, nous exhibons un algorithme en deux étapes : d'abord, l'énumération des mots valides (mots dont le score et suffisant) avec une approche par séparation et évaluation, puis la recherche simultanée et exacte de ces mots valides dans le texte. Nous comparons nos implémentations de ces algorithmes entre elles et montrons qu'elles sont utilisables en pratique. En particulier, l'algorithme par énumération s'avère rapidement le plus efficace, même en comparaison à un outil existant, puisque sa complexité est proportionnelle aux nombre d'occurrences produit en sortie. Les fonctions de recherche de di-PWM sont implantées dans un module en langage Python, d'installation et d'utilisation faciles, qui sera prochainement mis à disposition de la communauté sous licence libre.
Published: 2021

11. Necessary optimality condition for the minimal time crisis relaxing transverse condition via regularization

Author: Kenza Boumaza, Térence Bayen, Alain Rapaport, EA2151 Laboratoire de Mathématiques d'Avignon (LMA), Avignon Université (AU), Mathématiques, Informatique et STatistique pour l'Environnement et l'Agronomie (MISTEA), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Bourse de doctorat d'excellence algérienne, LabEx ’NUMEV’ incorporated into the I-Site ’MUSE’ (Montpellier), and Rapaport, Alain
Subjects: 0209 industrial biotechnology, Control and Optimization, Hybrid Maximum Principle, Boundary (topology), 02 engineering and technology, 01 natural sciences, Regularization (mathematics), Hamiltonian system, 020901 industrial engineering & automation, Maximum principle, Transverse crossing time, Convergence (routing), Regularization, Applied mathematics, Limit (mathematics), 0101 mathematics, Necessary optimality conditions, Mathematics, Sequence, Time crisis, Computer Science::Information Retrieval, 010102 general mathematics, [MATH.MATH-OC] Mathematics [math]/Optimization and Control [math.OC], Optimal control, Computational Mathematics, Control and Systems Engineering, [MATH.MATH-OC]Mathematics [math]/Optimization and Control [math.OC]
Abstract: We derive necessary optimality conditions for the time of crisis problem under a more general hypothesis than the usual one encountered in the hybrid setting, which requires that any optimal solution should cross the boundary of the constraint set transversely. Doing so, we apply the Pontryagin Maximum Principle to a sequence of regular optimal control problems whose integral cost approximates the time of crisis. Optimality conditions are derived by passing to the limit in the Hamiltonian system (without the use of the hybrid maximum principle). This convergence result essentially relies on the boundedness of the sequence of adjoint vectors in L∞. Our main contribution is to relate this property to the boundedness in L1 of a suitable sequence which allows to avoid the use of the transverse hypothesis on optimal paths. An example with non-transverse trajectories for which necessary conditions are derived highlights the use of this new condition.
Published: 2021

12. Towards a better understanding of grass bed dynamics using remote sensing at high spatial and temporal resolutions

Author: Estelle Pitard, Xavier Fortuny, Guillaume Papuga, Samuel Alleaume, Frédéric Andrieu, Marion Menu, Guilhem Debarros, Territoires, Environnement, Télédétection et Information Spatiale (UMR TETIS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire Charles Coulomb (L2C), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Conservatoire Botanique National Méditerranéen de Porquerolles, Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), ADENA - Réserve Naturelle Nationale du Bagnas, University of California [Berkeley] (UC Berkeley), University of California (UC), Agence de l'Eau ('appel a projet Biodiversite 2016'), University of Montpellier - AAP 2017-1-08, LabeX NUMEV - AAP 2017-1-08, UC Berkeley's Geospatial Innovation Facility (GIF), Université Paul-Valéry - Montpellier 3 (UPVM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University of California [Berkeley], and University of California
Subjects: 0106 biological sciences, National natural reserve of the bagnas (France), 010504 meteorology & atmospheric sciences, Occupancy, Stochastic modelling, Pondweed grass beds, [SDU.STU]Sciences of the Universe [physics]/Earth Sciences, Aquatic Science, Oceanography, Ecological indicator, 01 natural sciences, Resilience (network), Image resolution, Mesohaline lagoon, Ecosystem management, Wetlands conservation, 0105 earth and related environmental sciences, Remote sensing, Stuckenia pectinata, biology, 010604 marine biology & hydrobiology, Temporal survey, Sentinel-2 satellites, 15. Life on land, biology.organism_classification, Field (geography), [SDE]Environmental Sciences, Environmental science
Abstract: International audience; Wetlands conservation and resilience capacities are key issues in many places over the globe. Understanding these issues will benefit from a precise knowledge of seagrass species occupancy and coverage over time and over space. Such information can be obtained from remote sensing images and their classification thanks to a vegetation index, to be used in a complementary manner to field work inventories. Sentinel-2 data, which are available with a frequent revisit time (
Published: 2021

13. Parametric recurrence quantification analysis of autoregressive processes for pattern recognition in multichannel electroencephalographic data

Author: Stéphane Caron, Anthony Boyer, Frédéric Bouchara, François Bonnetblanc, Hugues Duffau, Annick Lesne, Sofiane Ramdani, Interactive Digital Humans (IDH), Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Contrôle Artificiel de Mouvements et de Neuroprothèses Intuitives (CAMIN), Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Cognition, Action, et Plasticité Sensorimotrice [Dijon - U1093] (CAPS), Université de Bourgogne (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM), Laboratoire d'Informatique et Systèmes (LIS), Aix Marseille Université (AMU)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Institut des Neurosciences de Montpellier (INM), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), Laboratoire de Physique Théorique de la Matière Condensée (LPTMC), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Institut de Génétique Moléculaire de Montpellier (IGMM), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), This research was supported by the LabEx NUMEV project (ANR-10-LABX-20) funded by the French government’s 'Investisse- ments d’Avenir' program managed by the French National Re- search Agency (ANR), grants from the Institut Universitaire de France, and INSERM laboratory (U1093)., ANR-10-LABX-0020,NUMEV,Digital and Hardware Solutions and Modeling for the Environement and Life Sciences(2010), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Institut des Neurosciences de Montpellier - Déficits sensoriels et moteurs (INM), Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU), and Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)
Subjects: [INFO.INFO-CC]Computer Science [cs]/Computational Complexity [cs.CC], Computer science, Recurrence quantification analysis, Physics::Medical Physics, [MATH.MATH-DS]Mathematics [math]/Dynamical Systems [math.DS], 02 engineering and technology, 01 natural sciences, [INFO.INFO-TS]Computer Science [cs]/Signal and Image Processing, Artificial Intelligence, 0103 physical sciences, Recurrence plots, 0202 electrical engineering, electronic engineering, information engineering, EEG Data, Asymptotic recurrence measures, [NLIN]Nonlinear Sciences [physics], [PHYS.COND.CM-SM]Physics [physics]/Condensed Matter [cond-mat]/Statistical Mechanics [cond-mat.stat-mech], 010306 general physics, Recurrence plot, Autoregressive stochastic processes, Parametric statistics, Series (mathematics), business.industry, Stochastic process, [SCCO.NEUR]Cognitive science/Neuroscience, Pattern recognition, Function (mathematics), Autoregressive model, Signal Processing, Pattern recognition (psychology), 020201 artificial intelligence & image processing, Computer Vision and Pattern Recognition, Artificial intelligence, business, Multichannel data, Software
Abstract: accepted 2020-08-04; International audience; Recurrence quantification analysis (RQA) is an acknowledged method for the characterization of experimental time series. We propose a parametric version of RQA, pRQA, allowing a fast processing of spatial arrays of time series, once each is modeled by an autoregressive stochastic process. This method relies on the analytical derivation of asymptotic expressions for five current RQA measures as a function of the model parameters. By avoiding the construction of the recurrence plot of the time series, pRQA is computationally efficient. As a proof of principle, we apply pRQA to pattern recognition in multichannel electroencephalographic (EEG) data from a patient with a brain tumor.
Published: 2021

14. Optimisation et prédiction de la production algale en polycultures, approches expérimentales et modélisation mathématique

Author: Krichen, Emna, Mathématiques, Informatique et STatistique pour l'Environnement et l'Agronomie (MISTEA), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), MARine Biodiversity Exploitation and Conservation (UMR MARBEC), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Labex NUMEV et ADEME, Université Montpellier, Alain Rapaport, Eric Fouilland, ANR-10-LABX-0020,NUMEV,Digital and Hardware Solutions and Modeling for the Environement and Life Sciences(2010), Rapaport, Alain, and Laboratoires d'excellence - Digital and Hardware Solutions and Modeling for the Environement and Life Sciences - - NUMEV2010 - ANR-10-LABX-0020 - LABX - VALID
Subjects: fluctuations des ressources, modélisation dynamique, microalgues, nitrogen, bactéries, interval estimation, biomasse, [INFO.INFO-BT]Computer Science [cs]/Biotechnology, bacteria, polycultures, azote, lumière, biomass, dynamical modeling, microalgae, estimation par intervalles, [MATH.MATH-OC] Mathematics [math]/Optimization and Control [math.OC], interactions, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, [SDE.BE] Environmental Sciences/Biodiversity and Ecology, [INFO.INFO-BT] Computer Science [cs]/Biotechnology, [INFO.INFO-MO] Computer Science [cs]/Modeling and Simulation, [MATH.MATH-OC]Mathematics [math]/Optimization and Control [math.OC], [SDE.BE]Environmental Sciences/Biodiversity and Ecology, resource fluctuations, light
Abstract: The stability and the performances of microalgae production systems are challenging issues, particularly in the context of the use of microalgae for the bioremediation of effluents and the production of biomass ofindustrial interest. One of the challenging axes of research is to take advantage of the diversity of microalgae through the use of assemblages (polycultures) for improving the overall production performances. However, theexploitation of these complex assemblages in an open system is subject to various stresses : biotic (undesirable microalgae or competing bacteria) and abiotic (limitation of resources, especially nitrogen and light). Thesestressing factors could influence interactions within assemblages, making thereby difficult the prediction and the optimization of the overall production. The objective of this thesis is to propose methods and tools forunderstanding, predicting, and optimizing the biomass production of an algal assemblage (natural or artificially designed microbial consortium) under the fluctuation of resources and culture conditions. More specifically,we have developed mathematical models based on dynamical systems that can be compared to laboratory and pilot-scale experiments. Firstly, an experimental method was defined for characterizing the specific growth rate of photosynthetic microorganisms, according to the limiting resource. Furthermore, a new functional estimation method is proposed. This method provides two growth curves that envelop scattering growth rate data and thus allow dynamic estimates of the state variables with guaranteed intervals. Secondly, the type of the interactions between two microalgae Chlorella sorokiniana and Scenedesmus pectinatus, which typically have successional trends in the outdoor ponds used for the treatment of urban wastewater, has been characterized ; first according to the fluctuation of the different forms of nitrogen (NH+4/NH3), and secondly to the light availability. The mathematical models associated with the experiments carried out during this thesis demonstrate that the initial development of an opportunistic microalgal species, which is more resistant to high levels of NH+4/NH3 was required for the subsequent development of a more efficient microalgal species under low light availability in these turbid processes. Third, we explored the paradoxical interactions occurring between microalgae and heterotrophic bacteria. Through the exudation of carbon, microalgae stimulate its competitors for common resources : nitrogen or phosphorus. We have thus studied the influence of this phenomenon by proposing a four-dimensional model. The mathematical analysis revealed that the equilibrium of coexistence is unique, and the installation of bacteria is robust, as it has been shown that the equilibrium without bacteria is unstable. We show that when the concentration of the mineral resource that continuously feeds the bioreactor is large enough, there are renewal rate values for which there is coexistence, while bacteria could not grow in the absence of microalgae under these same operating conditions. Finally, it has been shown, using simulations, that during coexistence their biomasses can oscillate. These results demonstrate the complexity of biotic interactions, provide methods applicable to other model organisms, and raise promising application possibilities for the optimization and the control of bioprocess dynamical systems for future work., Dans le contexte de l’utilisation des microalgues pour la bioremédiation d’effluents et la production de biomasse d’intérêt industriel, la stabilité et les performances des systèmes de production sont des enjeux majeurs. Unedes voies de recherche privilégiées est la mise à profit de la diversité des microalgues en assemblages (polycultures) pour l’amélioration des performances de la production. Néanmoins, l’exploitation de ces assemblages complexes en système ouvert extérieur est sujette à divers stress biotiques (microalgues indésirables ou bactéries compétitrices) et abiotiques (limitation des ressources, notamment l’azote et la lumière) qui influencent les interactions au sein des assemblages, rendant difficiles la prédiction et l’optimisation de la production. L’objectif de la présente thèse est de proposer des méthodes et des outils permettant de comprendre, prédire et optimiser la production de biomasse d’un assemblage algal (consortium microbien naturel ou artificiellement composé) sous la fluctuation des ressources et des conditions de culture. Plus particulièrement, nous avons développé des modèles mathématiques basés sur des systèmes dynamiques, qui peuvent être confrontés à des expériences en laboratoire et à l’échelle-pilote. Les premiers travaux de cette thèse ont consisté à choisir une méthode expérimentale pour la caractérisation de la vitesse de croissance spécifique des microorganismes photosynthétiques en fonction de la ressource limitante. Par ailleurs, une nouvelle méthode d’estimation fonctionnelle est proposée produisant deux courbes de croissance qui encadrent les données de vitesse de croissance et permettant ainsi des estimations dynamiques des variables d’état par intervalles garantis. Dans un deuxième temps, la nature des interactions entre deux microalgues Chlorella sorokiniana et Scenedesmus pectinatus, qui se succèdent classiquement dans les bassins extérieurs utilisés pour le traitement des eaux usées urbaines, a été caractérisée en fonction de la fluctuation des différentes formes de l’azote (NH+4/NH3) et ensuite de la lumière disponible. Les modèles mathématiques associés aux expérimentations menées au cours de cette thèse ont permis de démontrer que le développement initial d’une espèce microalgale de type opportuniste, plus résistante aux fortes teneurs en NH+4/NH3 était nécessaire pour que puisse s’établir ensuite une espèce microalgale plus efficace vis-à-vis de la faible lumière disponible dans ces procédés très turbides. Dans un troisième temps, nous avons exploré les interactions paradoxales qui existent entre les microalgues et les bactéries hétérotrophes. En effet, les microalgues stimulent, à travers l’exsudation du carbone, leurs compétiteurs pour une ressource commune : l’azote ou le phosphore. Nous avons étudié l’influence de ce phénomène en proposant un modèle dynamique en dimension quatre. L’analyse mathématique a révélé l’unicité de l’équilibre de coexistence et la robustesse de l’installation des bactéries, car il a été démontré que l’équilibre en absence de bactéries est répulsif. Nous montrons que lorsque la concentration de la ressource minérale alimentant en continu le bioréacteur est suffisamment grande, il existe des valeurs du taux de renouvellement du réacteur pour lesquelles il y a coexistence, alors que les bactéries ne pourraient pas se développer en l’absence de microalgues dans ces mêmes conditions opératoires. Enfin, il a été montré à l’aide de simulations que lors de la coexistence, leur biomasse respectives peut osciller. Ces résultats témoignent de la complexité des interactions biotiques, fournissent des méthodes applicables à d’autres organismes modèles permettant de les étudier, et soulèvent des possibilités d’application prometteuses pour l’optimisation et le contrôle des systèmes dynamiques de procédés pour les travaux futurs.
Published: 2020

15. Additive rheology of complex granular flows

Author: Thanh-Trung Vo, Farhang Radjai, Jean-Yves Delenne, Saeid Nezamabadi, Patrick Mutabaruka, Danang Architecture University (DAU), Physique et Mécanique des Milieux Divisés (PMMD), Laboratoire de Mécanique et Génie Civil (LMGC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Ingénierie des Agro-polymères et Technologies Émergentes (UMR IATE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Multiscale Material Science for Energy and Environment (MSE 2), Massachusetts Institute of Technology (MIT), Ministry of Education and Training in Vietnam, Campus France, and Labex NUMEV (University of Montpellier).
Subjects: Inertial frame of reference, Materials science, Science, General Physics and Astronomy, Atomic packing factor, 01 natural sciences, Texture (geology), General Biochemistry, Genetics and Molecular Biology, Article, 010305 fluids & plasmas, Stress (mechanics), Physics::Fluid Dynamics, Rheology, 0103 physical sciences, [SPI.MECA.MEMA]Engineering Sciences [physics]/Mechanics [physics.med-ph]/Mechanics of materials [physics.class-ph], Civil engineering, Colloids, lcsh:Science, 010306 general physics, Anisotropy, Multidisciplinary, Process chemistry, Physics, [SPI.MECA.BIOM]Engineering Sciences [physics]/Mechanics [physics.med-ph]/Biomechanics [physics.med-ph], General Chemistry, Mechanics, Condensed Matter::Soft Condensed Matter, lcsh:Q, Quasistatic process, Dimensionless quantity
Abstract: Granular flows are omnipresent in nature and industrial processes, but their rheological properties such as apparent friction and packing fraction are still elusive when inertial, cohesive and viscous interactions occur between particles in addition to frictional and elastic forces. Here we report on extensive particle dynamics simulations of such complex flows for a model granular system composed of perfectly rigid particles. We show that, when the apparent friction and packing fraction are normalized by their cohesion-dependent quasistatic values, they are governed by a single dimensionless number that, by virtue of stress additivity, accounts for all interactions. We also find that this dimensionless parameter, as a generalized inertial number, describes the texture variables such as the bond network connectivity and anisotropy. Encompassing various stress sources, this unified framework considerably simplifies and extends the modeling scope for granular dynamics, with potential applications to powder technology and natural flows., Granular materials are abundant in nature, but we haven’t fully understood their rheological properties as complex interactions between particles are involved. Here, Vo et al. show that granular flows can be described by a generalized dimensionless number based on stress additivity.
Published: 2020

16. Comprendre les spécificités physiques et vibro-mécaniques des Palissandres, bois du genre pantropical menacé Dalbergia

Author: Suarez Diaz, Sebastian, Guibal, Daniel, Cabrolier, Pierre, Thevenon, Marie-France, Langbour , Patrick, Brémaud, Iris, Bois (BOIS), Laboratoire de Mécanique et Génie Civil (LMGC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), BioWooEB (UPR BioWooEB), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Département Performances des systèmes de production et de transformation tropicaux (Cirad-PERSYST), Chercheur indépendant, Centre National de la Recherche Scientifique (CNRS), and Labex NUMEV
Subjects: bois, [PHYS.PHYS.PHYS-OPTICS]Physics [physics]/Physics [physics]/Optics [physics.optics], Palissandres, Dalbergia, propriétés vibro-mécaniques, artisanat, [SDE.ES]Environmental Sciences/Environmental and Society, colorimétrie, [PHYS.MECA.MEMA]Physics [physics]/Mechanics [physics]/Mechanics of materials [physics.class-ph], CITES, chémo-taxonomie, bois précieux, [PHYS.PHYS.PHYS-CHEM-PH]Physics [physics]/Physics [physics]/Chemical Physics [physics.chem-ph], usages, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, ComputingMilieux_MISCELLANEOUS
Abstract: International audience
Published: 2020

17. Comparative masticatory myology in anteaters and its implications for interpreting morphological convergence in myrmecophagous placentals

Author: Sérgio Ferreira-Cardoso, Frédéric Delsuc, Lionel Hautier, Pierre-Henri Fabre, Benoit de Thoisy, Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), The Natural History Museum [London] (NHM), Institut Pasteur de la Guyane, Réseau International des Instituts Pasteur (RIIP), Association Kwata - Etude et protection de la nature [Guyane], Sérgio Ferreira-Cardoso, Lionel Hautier and Frédéric Delsuc were supported by a European Research Council (ERC) consolidator grant (ConvergeAnt project #683257). Lionel Hautier and Frédéric Delsuc were supported by Centre National de la Recherche Scientifique (CNRS). This work was supported by 'Investissements d’Avenir' grants managed by Agence Nationale de la Recherche Labex CEBA (ANR-10-LABX-25-01), Labex CEMEB (ANR-10-LABX-0004), and Labex NUMEV (ANR-10-LABX-0020). The MRI platform member of the national infrastructure France-BioImaging is supported by the French National Research Agency (ANR-10-INBS-04, ‘Investments for the future’). The JAGUARS collection is supported through a FEDER/ERDF grant attributed to Kwata NGO, funded by the European Union, the Collectivité Territoriale de Guyane, and the DEAL Guyane., ANR-10-LABX-0025,CEBA,CEnter of the study of Biodiversity in Amazonia(2010), ANR-10-LABX-0004,CeMEB,Mediterranean Center for Environment and Biodiversity(2010), ANR-10-LABX-0020,NUMEV,Digital and Hardware Solutions and Modeling for the Environement and Life Sciences(2010), ANR-10-INBS-0004,France-BioImaging,Développment d'une infrastructure française distribuée coordonnée(2010), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE)
Subjects: 0106 biological sciences, Tamandua, Anatomy and Physiology, Masticatory apparatus, [SDV]Life Sciences [q-bio], lcsh:Medicine, Context (language use), 010603 evolutionary biology, 01 natural sciences, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, biology.animal, Cyclopedidae, 030304 developmental biology, 0303 health sciences, Anteater, Anteaters, biology, Comparative anatomy, General Neuroscience, lcsh:R, Tamandua tetradactyla, General Medicine, Anatomy, biology.organism_classification, Evolutionary Studies, Myrmecophagy, Myology, Jugal bone, Myrmecophagidae, General Agricultural and Biological Sciences, Convergence, Zoology
Abstract: BackgroundEcological adaptations of mammals are reflected in the morphological diversity of their feeding apparatus, which includes differences in tooth crown morphologies, variation in snout size, or changes in muscles of the feeding apparatus. The adaptability of their feeding apparatus allowed them to optimize resource exploitation in a wide range of habitats. The combination of computer-assisted X-ray microtomography (µ-CT) with contrast-enhancing staining protocols has bolstered the reconstruction of three-dimensional (3D) models of muscles. This new approach allows for accurate descriptions of muscular anatomy, as well as the quick measurement of muscle volumes and fiber orientation. Ant- and termite-eating (myrmecophagy) represents a case of extreme feeding specialization, which is usually accompanied by tooth reduction or complete tooth loss, snout elongation, acquisition of a long vermiform tongue, and loss of the zygomatic arch. Many of these traits evolved independently in distantly-related mammalian lineages. Previous reports on South American anteaters (Vermilingua) have shown major changes in the masticatory, intermandibular, and lingual muscular apparatus. These changes have been related to a functional shift in the role of upper and lower jaws in the evolutionary context of their complete loss of teeth and masticatory ability.MethodsWe used an iodine staining solution (I2KI) to perform contrast-enhanced µ-CT scanning on heads of the pygmy (Cyclopes didactylus), collared (Tamandua tetradactyla) and giant (Myrmecophaga tridactyla) anteaters. We reconstructed the musculature of the feeding apparatus of the three extant anteater genera using 3D reconstructions complemented with classical dissections of the specimens. We performed a description of the musculature of the feeding apparatus in the two morphologically divergent vermilinguan families (Myrmecophagidae and Cyclopedidae) and compared it to the association of morphological features found in other myrmecophagous placentals.ResultsWe found that pygmy anteaters (Cyclopes) present a relatively larger and architecturally complex temporal musculature than that of collared (Tamandua) and giant (Myrmecophaga) anteaters, but shows a reduced masseter musculature, including the loss of the deep masseter. The loss of this muscle concurs with the loss of the jugal bone in Cyclopedidae. We show that anteaters, pangolins, and aardvarks present distinct anatomies despite morphological and ecological convergences.
Published: 2020

18. Phase separation of polymer-bound particles induced by loop-mediated one dimensional effective long-range interactions

Author: Jean-Charles Walter, John Palmeri, Frédéric Geniet, Nils-Ole Walliser, Gabriel David, Jérôme Dorignac, Andrea Parmeggiani, Chase P. Broedersz, Laboratoire Charles Coulomb (L2C), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Arnold Sommerfeld Center for Theoretical Physics, Ludwig-Maximilians-Universität München, Ludwig-Maximilians-Universität München (LMU), Vrije Universiteit Amsterdam [Amsterdam] (VU), LPHI - Laboratory of Pathogen Host Interactions (LPHI), This project received partial financial support from theFrench Agence Nationale de la Recherche [Imaging andModeling Bacterial Mitosis (IBM) Project No. ANR-14-CE09-0025-01], the CNRS Défi Inphyniti (Projet StructurantNo. 2015–2016), and the LabEx NUMEV (ANR-10-LABX-0020) within the I-SITE MUSE of the Université deMontpellier [No. AAP 2013-2-005, No. 2015-2-055, No.2016-1-024, and Flagship Project Gene Expression Modeling(2017–2020)] (G.D., J.C.W., J.D., F.G., A.P., N.O.W., J.P.).G.D. acknowledges doctoral thesis and A.T.E.R postdoctoralsupport from the French Ministère de l’Enseignementsupérieur, de la Recherche et de l’Innovation. This work wassupported in part by a Modélisation pour le Vivant FrenchCNRS Grant (CoilChrom project). This project was alsosupported by the Deutsche Forschungsgemeinschaft (DFG)Grant No. TRR174 (C.P.B.)., and ANR-14-CE09-0025,IBM,Visualisation et Modélisation de la Mitose Bactérienne(2014)
Subjects: chemistry.chemical_classification, Physics, 0303 health sciences, Phase transition, Quantitative Biology::Biomolecules, Gaussian, Polymer, 01 natural sciences, 03 medical and health sciences, symbols.namesake, Variational method, chemistry, Chemical physics, Lattice (order), 0103 physical sciences, symbols, [PHYS.COND.CM-SM]Physics [physics]/Condensed Matter [cond-mat]/Statistical Mechanics [cond-mat.stat-mech], 010306 general physics, 030304 developmental biology, Phase diagram, Bacterial dna
Abstract: International audience; The cellular cytoplasm is organized into compartments. Phase separation is a simple manner to create membraneless compartments in order to confine and localize particles like proteins. In many cases, these particles are bound to fluctuating polymers like DNA or RNA. We propose a general theoretical framework for such polymer-bound particles and derive an effective 1D lattice gas model with both nearest-neighbor and emergent long-range interactions arising from looped configurations of the fluctuating polymer. We argue that 1D phase transitions exist in such systems for both Gaussian and self-avoiding polymers and, using a variational method that goes beyond mean-field theory, we obtain the complete mean occupation-temperature phase diagram. To illustrate this model, we apply it to the biologically relevant case of ParABS, a prevalent bacterial DNA segregation system.
Published: 2020

19. Insight into gluten structure in a mild chaotropic solvent by asymmetrical flow field-flow fractionation (AsFlFFF) and evidence of non-covalent assemblies between glutenin and ω-gliadin

Author: Marie-Hélène Morel, Ameur Louhichi, Frédéric Violleau, Paul Menut, Laurence Ramos, Amélie Banc, Justine Pincemaille, Edouard Chauveau, Ingénierie des Agro-polymères et Technologies Émergentes (UMR IATE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire Charles Coulomb (L2C), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Ecole d'Ingénieurs de Purpan (INPT - EI Purpan), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Paris-Saclay Food and Bioproduct Engineering (SayFood), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Chimie Agro-Industrielle (CAI), Ecole nationale supérieure des ingénieurs en arts chimiques et technologiques-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Doctoral School GAIA and the Labex Numev (ANR-10-LAB-20) for the funding of the PhD Grant, scientific council of Montpellier SupAgro, and ANR-18-CE06-0012,ELASTOBIO,Gels élastomériques de biopolymères soumis à des déformations extrêmes(2018)
Subjects: chemistry.chemical_classification, Molar mass, 010304 chemical physics, biology, General Chemical Engineering, Size-exclusion chromatography, food and beverages, 04 agricultural and veterinary sciences, General Chemistry, Polymer, 040401 food science, 01 natural sciences, Gluten, [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, Chaotropic agent, 0404 agricultural biotechnology, Glutenin, chemistry, Dynamic light scattering, Chemical engineering, 0103 physical sciences, biology.protein, Gliadin, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, Food Science
Abstract: International audience; Wheat gluten, one of the most complex viscoelastic protein networks in nature, is unique to get the specific texture of bread. Due to its complex protein composition, its insolubility in most solvents and the very high molar mass of half of the proteins (glutenin, the other half being gliadin), the architecture of the network is still not well understood. In this work, we have investigated model gluten protein extracts with contrasted compositions in glutenin and gliadin solubilized in a mild chaotropic solvent: ethanol/water (50/50 v/v). The samples display a liquid-liquid phase separation with an upper critical solution temperature that depends on the protein composition. The phase diagrams are consistent with the presence of supramolecular assemblies of proteins. To confirm the presence of these assemblies and fully characterize the objects dispersed in ethanol/water, we have used an asymmetrical flow field-flow fractionation (AsFlFFF) setup coupled with differential refractive index, multi-angle light scattering and dynamic light scattering detections to probe very dilute protein suspensions. We have identified three classes of objects, with distinctive molar mass, characteristic size and conformation: protein monomers, polymeric structures, and very loose protein assemblies with molar mass larger than 2.10 6 g/mol. A molecular characterization of the species by size exclusion chromatography in a denaturing solvent shows that polymers and assemblies are mainly composed of glutenin and ω-gliadin. The high content of ω-gliadin, devoid of cysteines, indicates the importance of non-covalent interactions involved in protein assemblies and might play a major role in gluten rheology
Published: 2020

20. Penalty function method for the minimal time crisis problem

Author: Kenza Boumaza, Alain Rapaport, Térence Bayen, Mathématiques, Informatique et STatistique pour l'Environnement et l'Agronomie (MISTEA), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), EA2151 Laboratoire de Mathématiques d'Avignon (LMA), Avignon Université (AU), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Bourse de doctorat d'excellence algérienne, LabEx ’NUMEV’ incorporated into the I-Site ’MUSE’ (Montpellier), and Bayen, Térence
Subjects: T57-57.97, 0209 industrial biotechnology, Mathematical optimization, Applied mathematics. Quantitative methods, Computer science, 010102 general mathematics, Control (management), [MATH.MATH-OC] Mathematics [math]/Optimization and Control [math.OC], 02 engineering and technology, 01 natural sciences, Set (abstract data type), 020901 industrial engineering & automation, Convergence (routing), QA1-939, Penalty method, [MATH.MATH-OC]Mathematics [math]/Optimization and Control [math.OC], 0101 mathematics, Mathematics
Abstract: International audience; In this note, we propose a new method to approximate the minimal time crisis problem using an auxiliary control and a penalty function, and show its convergence to a solution to the original problem. The interest of this approach is illustrated on numerical examples for which optimal trajectories can leave and enter the crisis set tangentially.; Dans cette note, nous proposons une nouvelle méthode pour approcher le problème du temps de crise en introduisant un contrôle additionnel et une fonction de pénalisation. Nous montronsla convergence des solutions approchées vers une solution du problème original. L’intérêt de cette approche est illustrée sur un exemple numérique pour lequel les trajectoires optimales peuvent entrerou sortir tangentiellement de l’ensemble de crise.
Published: 2020

21. A Note on Optimal and Sub-Optimal Feedback Controls for Biogas Production

Author: Antoine Haddon, Alain Rapaport, Héctor Ramírez, Mathématiques, Informatique et STatistique pour l'Environnement et l'Agronomie (MISTEA), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Departamento de Ingeniería Matemática [Santiago] (DIM), Universidad de Chile = University of Chile [Santiago] (UCHILE)-Centre National de la Recherche Scientifique (CNRS), Comision Nacional de Investigacion Cientifica y Tecnologica (CONICYT) 1160567, CONICYT FONDECYT 1160567, Basal Program from CONICYT-Chile : CMM-AFB 170001, Comision Nacional de Investigacion Cientifica y Tecnologica (CONICYT) : PFCHA/Doctorado Nacional/2017-21170249, and LabEx NUMEV incorporated into the I-Site MUSE
Subjects: Mathematical optimization, 021103 operations research, Control and Optimization, Singular Arc, Applied Mathematics, 0211 other engineering and technologies, 010103 numerical & computational mathematics, 02 engineering and technology, Management Science and Operations Research, 7. Clean energy, 01 natural sciences, Optimal control, Infinite horizon, Sub-optimality, [MATH.MATH-OC]Mathematics [math]/Optimization and Control [math.OC], 0101 mathematics, Biogas production, Mathematics, Chemostat model
Abstract: Comision Nacional de Investigacion Cientifica y Tecnologica (CONICYT) CONICYT FONDECYT 1160567 1160204 Basal Program from CONICYT-Chile CMM-AFB 170001 Comision Nacional de Investigacion Cientifica y Tecnologica (CONICYT) PFCHA/Doctorado Nacional/2017-21170249 LabEx NUMEV incorporated into the I-Site MUSE
Published: 2020

22. A multi observers approach when observability index is higher than the state dimension - a case study

Author: Alain Rapaport, Ihab Haidar, Jean-Pierre Barbot, Laboratoire QUARTZ (QUARTZ ), Université Paris 8 Vincennes-Saint-Denis (UP8)-Ecole Nationale Supérieure de l'Electronique et de ses Applications (ENSEA)-SUPMECA - Institut supérieur de mécanique de Paris-Ecole Internationale des Sciences du Traitement de l'Information (EISTI), Mathématiques, Informatique et STatistique pour l'Environnement et l'Agronomie (MISTEA), Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Université Paris 8 Vincennes-Saint-Denis (UP8)-SUPMECA - Institut supérieur de mécanique de Paris-Ecole Nationale Supérieure de l'Electronique et de ses Applications (ENSEA)-Ecole Internationale des Sciences du Traitement de l'Information (EISTI), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA), Université Paris 8 Vincennes-Saint-Denis (UP8)-Ecole Nationale Supérieure de l'Electronique et de ses Applications (ENSEA)-SUPMECA - Institut supérieur de mécanique de Paris (SUPMECA)-Ecole Internationale des Sciences du Traitement de l'Information (EISTI), ENSEA, LabEx NUMEV incorporated into the I-Site MUSE, and IEEE
Subjects: Estimation theory, optimisation, [MATH.MATH-DS]Mathematics [math]/Dynamical Systems [math.DS], Scalar (physics), Estimator, Systèmes dynamiques, Dynamical Systems, estimation d'erreur, Optimization and Control, Embedding, Applied mathematics, Gravitational singularity, Observability, Optimisation et contrôle, [MATH.MATH-OC]Mathematics [math]/Optimization and Control [math.OC], Mathematics
Abstract: International audience; We address a family of observation problems that would classically require the construction of an embedding, by a different approach which consists in the design of several estimators in parallel. In principle, for a dynamics in dimension n with a scalar output y, each estimator uses the knowledge of only n − 1 derivatives of the output, and the further derivatives are used to discriminate at any time among the estimators. Estimators are built here by roots tracking technique. We illustrate our approach on the parameter estimation of a polynomial dynamics. The simulations show that the final estimation jumps from one estimator to another when passing through observability singularities, or when the parameter suddenly changes, preserving a good estimation error.
Published: 2019

23. PALISSANDRES - Comprendre les liens botanique-chimie-mécanique-perception qui déterminent le statut de ‘bois précieux’ du genre pantropical menacé Dalbergia: Vers une co-conservation de la biodiversité et de la diversité culturelle artisanale?

Author: Brémaud, Iris, Langbour , Patrick, Jacques, Carbonneaux, Thevenon, Marie-France, Ramananantoandro, Tahiana, Quintanar Isaias, Alejandra, Bois (BOIS), Laboratoire de Mécanique et Génie Civil (LMGC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS), BioWooEB (UPR BioWooEB), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Département Performances des systèmes de production et de transformation tropicaux (Cirad-PERSYST), APLG - Association Professionnelle des Luthiers en Guitares, Université d'Antananarivo, Universidad Nacional Autónoma de México (UNAM), and Labex Numev
Subjects: [PHYS.MECA.VIBR]Physics [physics]/Mechanics [physics]/Vibrations [physics.class-ph], [SHS.MUSIQ]Humanities and Social Sciences/Musicology and performing arts, [PHYS.PHYS.PHYS-SOC-PH]Physics [physics]/Physics [physics]/Physics and Society [physics.soc-ph], Conservation, Mécanique, [SHS.ANTHRO-SE]Humanities and Social Sciences/Social Anthropology and ethnology, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, [SDE.ES]Environmental Sciences/Environmental and Society, Bois précieux tropicaux, [PHYS.MECA.MEMA]Physics [physics]/Mechanics [physics]/Mechanics of materials [physics.class-ph], Chimiodiversité, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Diversité biologique et culturelle, Artisanat
Abstract: National audience; RESUME : Les bois de Palissandres vrais (espèces du genre Dalbergia, famille des Fabaceae) représentent l'archétype des bois tropicaux précieux, emblématiques dans des usages culturels de différents métiers artisanaux, de différentes aires géoculturelles et différentes époques historiques, mais aujourd'hui menacés par une explosion de la consommation de type industrielle. Paradoxalement pour des bois aussi emblématiques, ils sont mal connus scientifiquement. Ce projet interdisciplinaire, international et inter-métiers considère le genre Dalbergia comme un système modèle pour l'étude de relations taxonomie-chimie-mécanique-usages-perception, pour comprendre ce qui les a rendus si recherchés, avec la volonté de contribuer à la co-conservation des diversités biologiques et socio-culturelles.
Published: 2019

24. Demonstration of facilitation between microalgae to face environmental stress

Author: Eric Fouilland, Emna Krichen, Emilie Le Floc'h, Alain Rapaport, Mathématiques, Informatique et STatistique pour l'Environnement et l'Agronomie (MISTEA), Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), MARine Biodiversity Exploitation and Conservation (UMR MARBEC), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut de Recherche pour le Développement (IRD), Agence de l'Environnement et de la Maîtrise de l'Energie (ADEME), Labex NUMEV, ADEME, Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA), and ANR-16-IDEX-0006,MUSE,MUSE(2016)
Subjects: 0106 biological sciences, 0301 basic medicine, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, Range (biology), Biodiversité et Ecologie, colonisation, [SDE.MCG]Environmental Sciences/Global Changes, lcsh:Medicine, Chlorella, Biotechnologies, Wastewater, Biology, Generalist and specialist species, Microbiology, 01 natural sciences, Environmental stress, Article, Water Purification, Biodiversity and Ecology, 03 medical and health sciences, Nutrient, Stress, Physiological, Microalgae, Colonization, microbiologie, lcsh:Science, Author Correction, modélisation, micro-algue, Chlorella sorokiniana, Multidisciplinary, Pioneer species, Ecology, 010604 marine biology & hydrobiology, lcsh:R, 15. Life on land, Modélisation et simulation, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, 030104 developmental biology, Modeling and Simulation, stress environnemental, Facilitation, lcsh:Q, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Water Microbiology, Scenedesmus, Biotechnology
Abstract: Author Correction: Demonstration of facilitation between microalgae to face environmental stress. In Scientific Reports, vol; 10, n°1, Article : 3557 ; DOI: 10.1038/s41598-020-59860-0 ; WOS:000563252500001 Author Correction: Demonstration of facilitation between microalgae to face environmental stress. In Scientific Reports, vol; 10, n°1, Article : 3557 ; DOI: 10.1038/s41598-020-59860-0 ; WOS:000563252500001The original version of this Article omitted an affiliation for Emna Krichen and the Acknowledgements section contained typographical errors and was incomplete. This erratum is available as an annex file.; International audience; Positive interactions such as facilitation play an important role during the biological colonization and species succession in harsh or changing environments. However, the direct evidence of such ecological interaction in microbial communities remains rare. Using common freshwater microalgae isolated from a High Rate Algal Pond HRAP treating wastewaters, we investigated with both experimental and modeling approaches the direct facilitation between two algal strains during the colonization phase. Our results demonstrate that the first colonization by microalgae under a severe chemical condition arose from the rapid growth of pioneer species such as Chlorella sorokiniana, which facilitated the subsequent colonization of low growth specialists such as Scenedesmus pectinatus. The pioneer species rapidly depleted the total available ammonia nitrogen favoring the specialist species initially inhibited by free ammonia toxicity. This latter species ultimately dominated the algal community through competitive exclusion under low nutrient conditions. We show that microbial successions are not only regulated by climatic conditions but also by interactions between species based on the ability to modify their growth conditions. We suggest that facilitation within the aquatic microbial communities is a widespread ecological interaction under a vast range of environmental stress.
Published: 2019

25. About overyielding with mixed cultures in batch processes

Author: Tibault Nidelet, Alain Rapaport, Jérôme Harmand, Laboratoire de Biotechnologie de l'Environnement [Narbonne] (LBE), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA), Mathématiques, Informatique et STatistique pour l'Environnement et l'Agronomie (MISTEA), Sciences Pour l'Oenologie (SPO), Université Montpellier 1 (UM1)-Institut de Recherche pour le Développement (IRD [Nouvelle-Calédonie])-Institut National de la Recherche Agronomique (INRA)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institut National de la Recherche Agronomique (INRA)-Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut de Recherche pour le Développement (IRD [Nouvelle-Calédonie])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), LabEx NUMEV incorporated into the I-Site MUSE, and Université Montpellier 1 (UM1)-Institut National de la Recherche Agronomique (INRA)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)
Subjects: 0209 industrial biotechnology, bioprocédé, Resource (biology), media_common.quotation_subject, [MATH.MATH-DS]Mathematics [math]/Dynamical Systems [math.DS], bioréacteur, 02 engineering and technology, Systèmes dynamiques, Competition (biology), 020901 industrial engineering & automation, 0202 electrical engineering, electronic engineering, information engineering, Economics, variable yield, [SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering, overyielding, competition, mortality, batch processes, Génie des procédés, media_common, 020208 electrical & electronic engineering, Modélisation et simulation, simulation, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, Dynamical Systems, Process Engineering, Control and Systems Engineering, Modeling and Simulation, Biochemical engineering
Abstract: International audience; This paper investigates-via modeling-several possible explanations of overyielding observed in mixed cultures cultivated in batch reactors. It is first shown that the classical model of competition of N species for a single resource cannot explain such overyielding. Then, three hypotheses are introduced and discussed at the light of numerical simulations.
Published: 2019

26. About modeling and control strategies for scheduling crop irrigation

Author: Kenza Boumaza, Carole Sinfort, Alain Rapaport, Sébastien Roux, Nesrine Kalboussi, Mathématiques, Informatique et STatistique pour l'Environnement et l'Agronomie (MISTEA), Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Information – Technologies – Analyse Environnementale – Procédés Agricoles (UMR ITAP), Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Euro-Mediterranean network TREASURE, LabEx NUMEV incorporated into the I-Site MUSE, ANR-16-CONV-0004,DIGITAG,Institut Convergences en Agriculture Numérique(2016), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), and ANR-16-CONV-0004,DigitAg,Digital Agriculture Convergence Lab(2016)
Subjects: 0209 industrial biotechnology, Irrigation, Mathematical optimization, Computer science, media_common.quotation_subject, State constraint, Scheduling (production processes), [SDV.SA.AGRO]Life Sciences [q-bio]/Agricultural sciences/Agronomy, Crop irrigation, 02 engineering and technology, irrigation, Scarcity, state constraint, optimal control, 020901 industrial engineering & automation, contrôle optimal, Optimization and Control, water management, 0202 electrical engineering, electronic engineering, information engineering, biomasse, Optimisation et contrôle, media_common, 020208 electrical & electronic engineering, Irrigation scheduling, simulation numérique, Optimal control, Agricultural sciences, Control and Systems Engineering, [MATH.MATH-OC]Mathematics [math]/Optimization and Control [math.OC], Sciences agricoles
Abstract: International audience; We propose a new simplified crop irrigation model and study the optimal control which consists in maximizing the biomass production at harvesting time, under a constraint on the total amount of water used. Under water scarcity, we show that a strategy with a singular arc can be better than a simple bang-bang control as commonly used. The gain is illustrated on numerical simulations. This result is a promising first step towards the application of control theory to the problem of optimal irrigation scheduling.
Published: 2019

27. Weighted minimum-length rearrangement scenarios

Author: Simonaitis, Pijus, Chateau, Annie, Swenson, Krister, École normale supérieure - Lyon (ENS Lyon), Méthodes et Algorithmes pour la Bioinformatique (MAB), Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), This work is partially supported by the Labex NUMEV flagship project GEM, and by the CNRS project Osez l’Interdisciplinarité., École normale supérieure de Lyon (ENS de Lyon), and Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Double cut and join (DCJ), Weighted genome rearrangement, 000 Computer science, knowledge, general works, Minimum-weight quadrangulation, Edge switch, Computer Science, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM]
Abstract: International audience; We present the first known model of genome rearrangement with an arbitrary real-valued weight function on the rearrangements. It is based on the dominant model for the mathematical and algorithmic study of genome rearrangement, Double Cut and Join (DCJ). Our objective function is the sum or product of the weights of the DCJs in an evolutionary scenario, and the function can be minimized or maximized. If the likelihood of observing an independent DCJ was estimated based on biological conditions, for example, then this objective function could be the likelihood of observing the independent DCJs together in a scenario. We present an O(n 4)-time dynamic programming algorithm solving the Minimum Cost Parsimonious Scenario (MCPS) problem for co-tailed genomes with n genes (or syntenic blocks). Combining this with our previous work on MCPS yields a polynomial-time algorithm for general genomes. The key theoretical contribution is a novel link between the parsimonious DCJ (or 2-break) scenarios and quadrangulations of a regular polygon. To demonstrate that our algorithm is fast enough to treat biological data, we run it on syntenic blocks constructed for Human paired with Chimpanzee, Gibbon, Mouse, and Chicken. We argue that the Human and Gibbon pair is a particularly interesting model for the study of weighted genome rearrangements.
Published: 2019

28. Experimental and theoretical study of the erosion of semi-crystalline polymers and the subsequent generation of microparticles

Author: Pascale Fabre, Thibaut Gaillard, Emmanuelle Gastaldi, Frédéric Nallet, Matthieu George, Laboratoire Charles Coulomb (L2C), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Ingénierie des Agro-polymères et Technologies Émergentes (UMR IATE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Centre de recherches Paul Pascal (CRPP), Centre National de la Recherche Scientifique (CNRS), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), LabEx NUMEV (2011-LABX-076), I-Site MUSE, and Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA)
Subjects: chemistry.chemical_classification, Microplastics, Materials science, Degradation kinetics, Kinetics, Pattern formation, 02 engineering and technology, General Chemistry, Polymer, 010402 general chemistry, 021001 nanoscience & nanotechnology, Condensed Matter Physics, Microstructure, 01 natural sciences, 0104 chemical sciences, chemistry, Erosion, [PHYS.COND.CM-MS]Physics [physics]/Condensed Matter [cond-mat]/Materials Science [cond-mat.mtrl-sci], Composite material, 0210 nano-technology, Joint (geology), [PHYS.COND.CM-SCM]Physics [physics]/Condensed Matter [cond-mat]/Soft Condensed Matter [cond-mat.soft], ComputingMilieux_MISCELLANEOUS
Abstract: International audience; The increase of plastics and microplastics in the environment is a major environmental challenge. Still, little is known about the degradation kinetics of macroplastics into smaller particles, under the joint actions of micro-organisms and physico-chemical factors, like UV or mechanical constraints. In order to gain insight into (bio)-degradation in various media, we perform accelerated erosion experiments by using a well-known enzymatic system. We show that the microstructure of semi-crystalline polymers plays a crucial role in the pattern formation at their surface. For the first time, the release of fragments of micrometric size is evidenced, through a mechanism that does not involve fracture propagation. A geometric erosion model allows a quantitative understanding of erosion rates and surface patterns, and provides a critical heterogeneity size, parting two types of behavior: spherulites either released, or eroded in situ. This new geometric approach could constitute a useful tool to predict the erosion kinetics and micro-particle generation in various media.
Published: 2019

29. NF-Y controls fidelity of transcription initiation at gene promoters through maintenance of the nucleosome-depleted region

Author: Oldfield, Andrew, Henriques, Telmo, Kumar, Dhirendra, Burkholder, Adam, Cinghu, Senthilkumar, Paulet, Damien, Bennett, Brian, Yang, Pengyi, Scruggs, Benjamin, Lavender, Christopher, Rivals, Eric, Adelman, Karen, Jothi, Raja, Epigenetics and Stem Cell Biology Laboratory [Durham] (ESCBL-NIEHS-NIH), National Institute of Environmental Health Sciences [Durham] (NIEHS-NIH), National Institutes of Health [Bethesda] (NIH)-National Institutes of Health [Bethesda] (NIH), Harvard Medical School [Boston] (HMS), Maharishi Valmiki Hospital, Méthodes et Algorithmes pour la Bioinformatique (MAB), Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Computationnelle (IBC), Institut National de la Recherche Agronomique (INRA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Marquette University, National Institutes of Health [Bethesda] (NIH), ATGC bioinformatics platform Montpellier. the Institut de Biologie Computationnelle (ANR-11-BINF-0002) Institut Français de Bioinformatique (ANR-11-INBS-0013)GEM Flagship project funded from Labex NUMEV (ANR-10-LABX-0020)France Génomique., ANR-10-LABX-0020/10-LABX-0020,NUMEV,Digital and Hardware Solutions and Modeling for the Environement and Life Sciences(2010), ANR-11-INBS-0013/11-INBS-0013,ReNaBi-IFB,Institut français de bioinformatique(2011), ANR-11-BINF-0002,IBC,Institut de Biologie Computationnelle de Montpellier(2011), ANR-10-INBS-09-01/10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS), Marquette University [Milwaukee], ANR-10-LABX-0020,NUMEV,Digital and Hardware Solutions and Modeling for the Environement and Life Sciences(2010), ANR-11-INBS-0013,IFB (ex Renabi-IFB),Institut français de bioinformatique(2011), ANR-11-BINF-0002,IBC,Institut de biologie Computationnelle(2011), and ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010)
Subjects: Site Transcription Initiation, [SDV.BC.BC]Life Sciences [q-bio]/Cellular Biology/Subcellular Processes [q-bio.SC], Small Interfering, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Chromatin, Nucleosomes, Promoter Regions, Mice, Metabolism, CCAAT-Binding Factor, Gene Knockdown Techniques, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], RNA, Transcription Initiation Site, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Embryonic Stem Cells
Abstract: International audience; Faithful transcription initiation is critical for accurate gene expression, yet the mechanisms underlying specific transcription start site (TSS) selection in mammals remain unclear. Here, we show that the histone-fold domain protein NF-Y, a ubiquitously expressed transcription factor, controls the fidelity of transcription initiation at gene promoters in mouse embryonic stem cells. We report that NF-Y maintains the region upstream of TSSs in a nucleosome-depleted state while simultaneously protecting this accessible region against aberrant and/or ectopic transcription initiation. We find that loss of NF-Y binding in mammalian cells disrupts the promoter chromatin landscape, leading to nucleosomal encroachment over the canonical TSS. Importantly, this chromatin rearrangement is accompanied by upstream relocation of the transcription pre-initiation complex and ectopic transcription initiation. Further, this phenomenon generates aberrant extended transcripts that undergo translation, disrupting gene expression profiles. These results suggest NF-Y is a central player in TSS selection in metazoans and highlight the deleterious consequences of inaccurate transcription initiation.
Published: 2019

30. Demonstration of a facilitation between microalgae to face ammonia toxicity in a High Rate Algal Pond

Author: Krichen, Emna, Lefloc'H, Emilie, Rapaport, Alain, Fouilland, Éric, Mathématiques, Informatique et STatistique pour l'Environnement et l'Agronomie (MISTEA), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA), MARine Biodiversity Exploitation and Conservation (UMR MARBEC), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Labex Numev, ADME, Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Universidad de Valladolid (Valladolid). Valladolid, ESP., and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)
Subjects: [SDE.IE]Environmental Sciences/Environmental Engineering, fungi, [MATH.MATH-DS]Mathematics [math]/Dynamical Systems [math.DS], food and beverages, [SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation
Abstract: International audience; The use of intensive microalgae cultivation for both wastewater treatment and valorization of the produced algal biomass has received increased attention in the literature. Maintaining the stability and economic viability of the algal production during the wastewater treatment process is of crucial importance. However, the presence of growth inhibitors in untreated sewage may damage the algae culture. Ammonia NH3 is considered as an inhibitor of photosynthesis at high pH that can cause failure of high rate oxidation ponds when supplemented with substantial concentrations of ammonium NH4+.Many studies highlighted the effects of high ammonium concentrations on growth, which vary significantly within classes of microalgae and within species. However, little is known about interactions between species under a potentially toxic environment and no studies have reported the effect of ammonia toxicity on algal species successions which impact the performance of the waste removal process. We hypothesize that an ecological facilitation can occur between two microalgae, when one species being more tolerant to ammonia can contribute to reduce the ammonium availability, making the growth of more sensitive microalgae possible. Such hypothesis has been suggested to explain the widely observed succession of Chlorella sp. and Scenedesmus sp. reported in High Rate Algal Ponds supplemented with urban wastewaters.
Published: 2019

31. Linking BWT and XBW via Aho-Corasick Automaton: Applications to Run-Length Encoding

Author: Cazaux, Bastien, Rivals, Eric, Méthodes et Algorithmes pour la Bioinformatique (MAB), Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Institut de Biologie Computationnelle (IBC), Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS), Support from the Institut de Biologie Computationnelle (ANR-11-BINF-0002).Eric Rivals: thanks the GEM Flagship project funded from Labex NUMEV (ANR-10-LABX-0020)., University of Pisa, Nadia Pisanti, Solon P. Pissis, ANR-11-BINF-0002,IBC,Institut de biologie Computationnelle(2011), ANR-10-LABX-0020,NUMEV,Digital and Hardware Solutions and Modeling for the Environement and Life Sciences(2010), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), ANR-11-BINF-0002,IBC,Institut de Biologie Computationnelle de Montpellier(2011), and ANR-10-LABX-0020/10-LABX-0020,NUMEV,Digital and Hardware Solutions and Modeling for the Environement and Life Sciences(2010)
Subjects: Run Length Encoding (RLE), Aho-Corasick automaton, Aho-Corasick Tree, [INFO.INFO-DS]Computer Science [cs]/Data Structures and Algorithms [cs.DS], Burrows Wheeler Transform, Compression, XBWT, [INFO.INFO-DM]Computer Science [cs]/Discrete Mathematics [cs.DM], Data Structures, Algorithm, 2012 ACM Subject Classification Mathematics of computing → Discrete mathematics, Theory of computation → Randomness, geometry and discrete structures, Theory of computation → Data structures and algorithms for data management, Indexing, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Stringology
Abstract: URN: urn:nbn:de:0030-drops-104955URL: http://drops.dagstuhl.de/opus/volltexte/2019/10495/ISBN ={978-3-95977-103-0},ISSN ={1868-8969},; International audience; The boom of genomic sequencing makes compression of sets of sequences inescapable. This underlies the need for multi-string indexing data structures that helps compressing the data. The most prominent example of such data structures is the Burrows-Wheeler Transform (BWT), a reversible permutation of a text that improves its compressibility. A similar data structure, the eXtended Burrows-Wheeler Transform (XBW), is able to index a tree labelled with alphabet symbols. A link between a multi-string BWT and the Aho-Corasick automaton has already been found and led to a way to build a XBW from a multi-string BWT. We exhibit a stronger link between a multi-string BWT and a XBW by using the order of the concatenation in the multi-string. This bijective link has several applications: first, it allows one to build one data structure from the other; second, it enables one to compute an ordering of the input strings that optimises a Run-Length measure (i.e., the compressibility) of the BWT or of the XBW.
Published: 2019

32. Hierarchical Space-Time Modeling of Asymptotically Independent Exceedances With an Application to Precipitation Data

Author: Gwladys Toulemonde, Carlo Gaetan, Jean-Noël Bacro, Thomas Opitz, Institut Montpelliérain Alexander Grothendieck (IMAG), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Dipartimento di Scienze Ambientali, Informatica e Statistica [Venezia] (DAIS), University of Ca’ Foscari [Venice, Italy], Biostatistique et Processus Spatiaux (BIOSP), Institut National de la Recherche Agronomique (INRA), Littoral, Environnement : Méthodes et Outils Numériques (LEMON), Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Université de Montpellier (UM), Centre National de la Recherche Scientifique (CNRS), Biostatistique et Processus Spatiaux (BioSP), Littoral, Environment: MOdels and Numerics (LEMON), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut Montpelliérain Alexander Grothendieck (IMAG), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Hydrosciences Montpellier (HSM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), French National Programme LEFE/INSU, LabEx NUMEV, financial support from Ca’ Foscari University, Italy, and Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)
Subjects: Statistics and Probability, Quasi-maximum likelihood, Computer science, 01 natural sciences, Composite likelihood, 010104 statistics & probability, Asymptotic independence, Gamma random fields, Hourly precipitation, Space-time convolution, Space-time extremes, [MATH.MATH-ST]Mathematics [math]/Statistics [math.ST], 0502 economics and business, Precipitation, Statistical physics, 0101 mathematics, 050205 econometrics, [STAT.AP]Statistics [stat]/Applications [stat.AP], Symptotic independence, Space time, 05 social sciences, Statistical model, [STAT.TH]Statistics [stat]/Statistics Theory [stat.TH], [STAT]Statistics [stat], Event data, Key (cryptography), Statistics, Probability and Uncertainty, Settore SECS-S/01 - Statistica
Abstract: International audience; The statistical modeling of space-time extremes in environmental applications is key to understanding complex dependence structures in original event data and to generating realistic scenarios for impact models. In this context of high-dimensional data, we propose a novel hierarchical model for high threshold exceedances defined over continuous space and time by embedding a space-time Gamma process convolution for the rate of an exponential variable, leading to asymptotic independence inspace and time. Its physically motivated anisotropic dependence structure is based on geometric objects moving through space-time according to a velocity vector. We demonstrate that inference based on weighted pairwise likelihood is fast and accurate. The usefulness of our model is illustrated by an application to hourly precipitation data from a study region in Southern France, where it clearly improves on an alternative censored Gaussian space-time random field model. While classical limit models based on threshold-stability fail to appropriately capture relatively fast joint tail decay rates between asymptotic dependence and classical independence, strong empirical evidence from our application and other recent case studies motivates the use of more realistic asymptotic independence models such as ours.
Published: 2019

33. Tackling the question of specific interactions in a complex blend of Proteins

Author: Morel, Marie Helene, Banc, Amélie, VIOLLEAU, Frédéric, Menut, Paul, Pincemaille, Justine, Ramos, Laurence, Ingénierie des Agro-polymères et Technologies Émergentes (UMR IATE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Laboratoire Charles Coulomb (L2C), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Chimie Agro-Industrielle (CAI), Institut National de la Recherche Agronomique (INRA)-Ecole nationale supérieure des ingénieurs en arts chimiques et technologiques-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Ingénierie, Procédés, Aliments (GENIAL), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Financement labex Numev, Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), ProdInra, Archive Ouverte, Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA), Institut National Polytechnique (Toulouse) (Toulouse INP), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole nationale supérieure des ingénieurs en arts chimiques et technologiques-Institut National de la Recherche Agronomique (INRA)
Subjects: polypeptide, [SDV.IDA]Life Sciences [q-bio]/Food engineering, interaction protéique, Flow Field Flow Fractionation, [SDV.IDA] Life Sciences [q-bio]/Food engineering, gluten de blé, gliadine
Abstract: Tackling the question of specific interactions in a complex blend of Proteins. Edible Soft Matter – a SoftComp Topical Workshop
Published: 2019

34. High performance text indexing and applications in life sciences

Author: Rivals, Eric, Institut de Biologie Computationnelle (IBC), Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS), Méthodes et Algorithmes pour la Bioinformatique (MAB), Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Flagship project GEM (Gene Expression Modelling) funded by Labex NUMEV, ANR-10-LABX-0020,NUMEV,Digital and Hardware Solutions and Modeling for the Environement and Life Sciences(2010), Institut National de la Recherche Agronomique (INRA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), and ANR-10-LABX-0020/10-LABX-0020,NUMEV,Digital and Hardware Solutions and Modeling for the Environement and Life Sciences(2010)
Subjects: Bioinformatics, Data structure, NGS, Query, Services, Sequencing, Indexing, Efficiency, Genomics, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM]
Abstract: International audience; Large corpura of texts or of sequences serve as references and are interrogated through web site or programming interfaces. In life sciences, new sequencing technologies have revolutionised the acquisition of genomic sequences and triggered an exponential accumulation of reference sequences in international, public databases. Several kinds of text queries form the basic operation of programs that analyse genomic sequences. For instance, the webserver of EMBL-EBI receives 27 million queries a day. A typical sequencing experiment yields a hundred million sequencing reads-about 150 nucleotides long-each of which needs to be compared to a reference genome. To analyse such data or to mine public sequence repositories demands very efficient programs and algorithms. Only, the use of complex and specific, indexing data structures allows us to match the needs of Life sciences communities. I will present some indexing data structures that enables high performance computational analyses in genomics, and mention their pracical applications. Beyond text data, such data structures can be adapted to index other types of discrete data like trees or graphs. This will be key for the development of computational pan-genomics.
Published: 2019

35. 4D compressive sensing holographic microscopy imaging of small moving objects

Author: Nitin Rawat, Michel Gross, Daniel Alexandre, Alexey Brodoline, Nicolas Cubedo, Brodoline, Alexey, Laboratoires d'excellence - Digital and Hardware Solutions and Modeling for the Environement and Life Sciences - - NUMEV2010 - ANR-10-LABX-0020 - LABX - VALID, Laboratoire Charles Coulomb (L2C), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Electrical & Computer Engineering Department [Storrs, CT, USA], University of Connecticut (UCONN), Mécanismes moléculaires dans les démences neurodégénératives (MMDN), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), We acknowledge Corinne Fournier and Laurent Daudet for fruitful discussions, and LabEx NUMEV (ANR-10-LABX-20 , French National Research Agency: Micro Holo 4D) and CNRS ( Dé: Instrumentation aux limites 2018 ) for funding., ANR-10-LABX-0020,NUMEV,Digital and Hardware Solutions and Modeling for the Environement and Life Sciences(2010), Université de Montpellier (UM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École pratique des hautes études (EPHE), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)
Subjects: Physics, [PHYS.PHYS.PHYS-OPTICS] Physics [physics]/Physics [physics]/Optics [physics.optics], Laser scattering, [PHYS.PHYS.PHYS-OPTICS]Physics [physics]/Physics [physics]/Optics [physics.optics], business.industry, Scattering, Holography, 02 engineering and technology, 021001 nanoscience & nanotechnology, 01 natural sciences, Atomic and Molecular Physics, and Optics, law.invention, 010309 optics, Optics, Compressed sensing, Three dimensional imaging, law, 0103 physical sciences, Microscopy, Digital holographic microscopy, 0210 nano-technology, business
Abstract: International audience; We show that compressive sensing (CS) calculations are very ecient to reconstruct in 3D sparse objects whose 2D hologram has been recorded by digital holographic microscopy. The method is well adapted to image small scattering objects moving within a larger motionless object. This situation corresponds to red blood cells (RBCs) circulating in the vascular system of a zebrash (Danio rerio) larva. RBCs positions are imaged in 3D from a single hologram, while the RBCs trajectories, i.e. the perfused blood vessels, are imaged from a sequence of holograms. With respect to previous work (Donnarumma et al., Opt. express, 24, 26887, 2016), we get a gain of ∼ 500 in calculation speed.
Published: 2019

36. Cyprinid herpesvirus 3 Evolves In Vitro through an Assemblage of Haplotypes that Alternatively Become Dominant or Under-Represented

Author: Klafack, Sandro, Fiston-Lavier, Anna-Sophie, Bergmann, Sven M., Hammoumi, Saliha, Schröder, Lars, Fuchs, Walter, Lusiastuti, Angela, Lee, Pei-Yu, Heredia, Sarahi Vega, consortium, Master student consortium Master student, Gosselin-Grenet, Anne-Sophie, Avarre, Jean-Christophe, Institute of Infectology, Federal Research Institute for Animal Health - Friedrich-Loeffler-Institut, Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UR226, Institute of Molecular Virology and Cell Biology, Research Institute for Freshwater Aquaculture and Fisheries Extension, GenReach Biotechnology, Diversité, Génomes & Interactions Microorganismes - Insectes [Montpellier] (DGIMI), Université de Montpellier (UM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Institut National de la Recherche Agronomique (INRA), Friedrich-Loeffler-Institut, ANR-11-EMID-0006,MOLTRAQ(2011), ANR-10-LABX-0020,NUMEV,Digital and Hardware Solutions and Modeling for the Environement and Life Sciences(2010), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM), Bergmann, Sven, Avarre, Jean-Christophe, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), ERA-NET EMIDA [ANR-11-EMIDA-006], and LabEx NUMEV [ANR 10 LABX-00-76]
Subjects: 0301 basic medicine, Biodiversité et Ecologie, Cyprinid herpesvirus 3, 030106 microbiology, ved/biology.organism_classification_rank.species, lcsh:QR1-502, Virulence, virus, Biology, Article, lcsh:Microbiology, Virus, Biodiversity and Ecology, 03 medical and health sciences, Common carp, cell culture passages, haplotype sequence, Virology, Digital polymerase chain reaction, analyse génomique, virus evolution, Genetics, ved/biology, Haplotype, herpes, DNA virus, herpes simplex, 3. Good health, virulence, 030104 developmental biology, Infectious Diseases, Viral evolution, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: Viruses are able to evolve in vitro by mutations after serial passages in cell cultures, which can lead to either a loss, or an increase, of virulence. Cyprinid herpesvirus 3 (CyHV-3), a 295-kb double-stranded DNA virus, is the etiological agent of the koi herpesvirus disease (KHVD). To assess the influence of serial passages, an isolate of CyHV-3 (KHV-T) was passaged 99 times onto common carp brain (CCB) cells, and virus virulence was evaluated during passages through the experimental infections of common carp. After 78 CCB passages, the isolate was much less virulent than the original form. A comparative genomic analysis of these three forms of KHV-T (P0, P78 and P99) revealed a limited number of variations. The largest one was a deletion of 1363 bp in the predicted ORF150, which was detected in P78, but not in P99. This unexpected finding was confirmed by conventional PCR and digital PCR. The results presented here primarily suggest that, CyHV-3 evolves, at least in vitro, through an assemblage of haplotypes that alternatively become dominant or under-represented.
Published: 2019

37. Phase separation dynamics of gluten protein mixtures

Author: Amélie Banc, Paul Menut, Marie Helene Morel, Marie-Sousai Appavou, Edouard Chauveau, Justine Pincemaille, Laurence Ramos, Salvatore Costanzo, Laboratoire Charles Coulomb (L2C), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Ingénierie des Agro-polymères et Technologies Émergentes (UMR IATE), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA), Jülich Centre for Neutron Science (JCNS), Ingénierie, Procédés, Aliments (GENIAL), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Labex Numev (ANR-10-LAB-20), Banc, A., Pincemaille, J., Costanzo, S., Chauveau, E., Appavou, M. -S., Morel, M. -H., Menut, P., Ramos, L., Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)
Subjects: Work (thermodynamics), Materials science, Glutens, gluténine, Spinodal decomposition, Thermodynamics, FOS: Physical sciences, 02 engineering and technology, Condensed Matter - Soft Condensed Matter, Chemical Fractionation, 010402 general chemistry, 01 natural sciences, Viscoelasticity, law.invention, Viscosity, Glutenin, law, synchrotron, [SDV.IDA]Life Sciences [q-bio]/Food engineering, Scattering, Radiation, ddc:530, chemistry.chemical_classification, biology, Scattering, Temperature, viscoélasticité, General Chemistry, 021001 nanoscience & nanotechnology, Condensed Matter Physics, Gluten, Synchrotron, 0104 chemical sciences, 3. Good health, Condensed Matter::Soft Condensed Matter, chemistry, gluten, biology.protein, Soft Condensed Matter (cond-mat.soft), 0210 nano-technology, Synchrotrons, glutenin, procédé de séparation
Abstract: We investigate by time-resolved Synchrotron ultra-small X-ray scattering the dynamics of liquid-liquid phase-separation (LLPS) of gluten protein suspensions following a temperature quench. Samples at a fixed concentration (237 mg/ml) but with different protein compositions are investigated. In our experimental conditions, we show that fluid viscoelastic samples depleted in polymeric glutenin phase-separate following a spinodal decomposition process. We quantitatively probe the late stage coarsening that results from a competition between thermodynamics that speeds up the coarsening rate as the quench depth increases, and transport that slows downs the rate. For even deeper quenches, the even higher viscoelasticity of the continuous phase leads to a "quasi" arrested phase separation. Anomalous phase-separation dynamics is by contrast measured for a gel sample rich in glutenin, due to elastic constraints. This work illustrates the role of viscoelasticity in the dynamics of LLPS in protein dispersions., Comment: accepted for publication in Soft Matter
Published: 2019

38. Axe Modélisation, LabEx NUMEV

Author: Palmeri, John, Jourdan, Franck, Laboratoire Charles Coulomb (L2C), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Biomécanique des Interactions et de l'Organisation des Tissus et des Cellules (BIOTIC), Laboratoire de Mécanique et Génie Civil (LMGC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), and LabEx NUMEV
Subjects: [PHYS.PHYS.PHYS-BIO-PH]Physics [physics]/Physics [physics]/Biological Physics [physics.bio-ph], [PHYS.COND.CM-SM]Physics [physics]/Condensed Matter [cond-mat]/Statistical Mechanics [cond-mat.stat-mech], [PHYS.COND.CM-SCM]Physics [physics]/Condensed Matter [cond-mat]/Soft Condensed Matter [cond-mat.soft]
Abstract: National audience; Présentation des activités de l’axe Modélisation, LabEx NUMEV
Published: 2018

39. Control of Two Manipulator Arms of an Underwater Robot for Deep-Sea Manipulation of Deformable Biological Samples

Author: Leborne, François, Département Systèmes Sous-Marins - IFREMER, Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Conception et commande de robots pour la manipulation (DEXTER), Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), LABEX NUMEV, Université de Montpellier, Vincent Creuze, Lorenzo Brignone (co-encadrant), Ahmed Chemori (co-encadrant), and Ifremer et LIRMM
Subjects: Force Sensing, Robotique sous-marine, mesure d’effort, manipulation, Modeling, identification, Underwater Robotics, modélisation, [SPI.AUTO]Engineering Sciences [physics]/Automatic
Abstract: The research carried out in the scope of this doctorate degree aims to develop innovativetechniques to improve the collection of biological and mineral samples underwaterusing robotic manipulators. The end goal is to enhance the handling by robotic means inorder tomaximise sample quality provided to marine scientists. The proposed techniquesare based on an in-depth analysis of the robotic arm actuators used in most recent underwaterintervention vehicles, in order to improve the accuracy of the positionning of thetools held by the manipulator arms. An instrumented tool has also been developed withthe aim to measure the reaction forces and adapt the interaction between the arm’s endeffectorand its environment to improve samples handling. These methods and the othercontributions described in this thesis have been experimentally validated using Ifremer’shybrid-ROV Ariane equipped with two electrically actuated heterogeneous robotic arms.; Dans le cadre de la collecte sous-marine d’échantillons biologiques et minéraux pour larecherche scientifique par un robot sous-marin équipé de bras manipulateurs, ce projet dethèse a pour but principal le développement de nouvelles techniques demanipulation deséchantillons, plus fiables, permettant d’en assurer l’intégrité physique et leur exploitabilitépar les chercheurs. Les nouvelles techniques de manipulation proposées prennent encompte l’actionnement particulier des nouveaux bras électriques sous-marins équipantles engins récents, afin d’augmenter la précision du positionnement des outils embarquéspar le manipulateur. Un outil amovible, compliant, et mesurant les efforts d’interactionentre les bras du sous-marin et leur environnement est aussi proposé, et des méthodes permettantde tirer partie des caractéristiques de cet outil sont développées et testées expérimentalement.L’engin sous-marin hybride HROV Ariane, équipé de deux bras électriqueshétérogènes, offre la plateforme opérationnelle pour la validation expérimentale des solutionsproposées.
Published: 2018

40. Contributions à la commande de deux bras manipulateurs d'un robot sous-marin pour la manipulation à grande profondeur d'échantillons biologiques déformables

Author: Leborne, François, Département Systèmes Sous-Marins - IFREMER, Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Conception et commande de robots pour la manipulation (DEXTER), Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), LABEX NUMEV, Université de Montpellier, Vincent Creuze, Lorenzo Brignone (co-encadrant), Ahmed Chemori (co-encadrant), and Ifremer et LIRMM
Subjects: Force Sensing, Robotique sous-marine, mesure d’effort, manipulation, Modeling, identification, Underwater Robotics, modélisation, [SPI.AUTO]Engineering Sciences [physics]/Automatic
Abstract: The research carried out in the scope of this doctorate degree aims to develop innovativetechniques to improve the collection of biological and mineral samples underwaterusing robotic manipulators. The end goal is to enhance the handling by robotic means inorder tomaximise sample quality provided to marine scientists. The proposed techniquesare based on an in-depth analysis of the robotic arm actuators used in most recent underwaterintervention vehicles, in order to improve the accuracy of the positionning of thetools held by the manipulator arms. An instrumented tool has also been developed withthe aim to measure the reaction forces and adapt the interaction between the arm’s endeffectorand its environment to improve samples handling. These methods and the othercontributions described in this thesis have been experimentally validated using Ifremer’shybrid-ROV Ariane equipped with two electrically actuated heterogeneous robotic arms.; Dans le cadre de la collecte sous-marine d’échantillons biologiques et minéraux pour larecherche scientifique par un robot sous-marin équipé de bras manipulateurs, ce projet dethèse a pour but principal le développement de nouvelles techniques demanipulation deséchantillons, plus fiables, permettant d’en assurer l’intégrité physique et leur exploitabilitépar les chercheurs. Les nouvelles techniques de manipulation proposées prennent encompte l’actionnement particulier des nouveaux bras électriques sous-marins équipantles engins récents, afin d’augmenter la précision du positionnement des outils embarquéspar le manipulateur. Un outil amovible, compliant, et mesurant les efforts d’interactionentre les bras du sous-marin et leur environnement est aussi proposé, et des méthodes permettantde tirer partie des caractéristiques de cet outil sont développées et testées expérimentalement.L’engin sous-marin hybride HROV Ariane, équipé de deux bras électriqueshétérogènes, offre la plateforme opérationnelle pour la validation expérimentale des solutionsproposées.
Published: 2018

41. Alterations of EEG rhythms during motor preparation following awake brain surgery

Author: Bénédicte Poulin-Charronnat, Anthony Boyer, Sofiane Ramdani, David Guiraud, Hugues Duffau, François Bonnetblanc, Control of Artificial Movement and Intuitive Neuroprosthesis ( CAMIN ), Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier ( LIRMM ), Université de Montpellier ( UM ) -Centre National de la Recherche Scientifique ( CNRS ) -Université de Montpellier ( UM ) -Centre National de la Recherche Scientifique ( CNRS ) -Inria Sophia Antipolis - Méditerranée ( CRISAM ), Institut National de Recherche en Informatique et en Automatique ( Inria ) -Institut National de Recherche en Informatique et en Automatique ( Inria ), Efficience Déficience Motrice [Montpellier] ( EDM ), Université Montpellier 1 ( UM1 ), Hôpital Gui de Chauliac, Université Montpellier 1 ( UM1 ) -Centre Hospitalier Régional Universitaire [Montpellier] ( CHRU Montpellier ), Equipe Perception et cognition musicales, Sciences et Technologies de la Musique et du Son ( STMS ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -IRCAM-Centre National de la Recherche Scientifique ( CNRS ) -Université Pierre et Marie Curie - Paris 6 ( UPMC ) -IRCAM-Centre National de la Recherche Scientifique ( CNRS ), Cognition, Action, et Plasticité Sensorimotrice [Dijon - U1093] ( CAPS ), Université de Bourgogne ( UB ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ), ANR-10-LABX-0020/10-LABX-0020,NUMEV,Digital and Hardware Solutions and Modeling for the Environement and Life Sciences ( 2010 ), Control of Artificial Movement and Intuitive Neuroprosthesis (CAMIN), Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Interactive Digital Humans (IDH), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Hôpital Gui de Chauliac [CHU Montpellier], Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier), Institut des Neurosciences de Montpellier (INM), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), Laboratoire d'Etude de l'Apprentissage et du Développement [Dijon] (LEAD), Université de Bourgogne (UB)-Centre National de la Recherche Scientifique (CNRS), Cognition, Action, et Plasticité Sensorimotrice [Dijon - U1093] (CAPS), Université de Bourgogne (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Universitaire de France (IUF), Ministère de l'Education nationale, de l’Enseignement supérieur et de la Recherche (M.E.N.E.S.R.), LabEx NUMEV project by the French government's 'Investissements d'Avenir' program ANR-10-LABX-20 Institut Universitaire de France INSERM laboratory U1093, ANR-10-LABX-0020,NUMEV,Digital and Hardware Solutions and Modeling for the Environement and Life Sciences(2010), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Inria Sophia Antipolis - Méditerranée (CRISAM), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Université Montpellier 1 (UM1)-Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier), Institut des Neurosciences de Montpellier - Déficits sensoriels et moteurs (INM), and Centre National de la Recherche Scientifique (CNRS)-Université de Bourgogne (UB)
Subjects: Adult, Male, medicine.medical_specialty, Cognitive Neuroscience, [SDV.CAN]Life Sciences [q-bio]/Cancer, Experimental and Cognitive Psychology, Spectral analysis, 050105 experimental psychology, [ SDV.CAN ] Life Sciences [q-bio]/Cancer, Lesion, 03 medical and health sciences, Cognition, 0302 clinical medicine, Arts and Humanities (miscellaneous), Awake brain surgery, Reaction Time, Developmental and Educational Psychology, medicine, Humans, 0501 psychology and cognitive sciences, Brainwaves, Wakefulness, Balance (ability), Brain Neoplasms, [SCCO.NEUR]Cognitive science/Neuroscience, 05 social sciences, Healthy subjects, Brain, Electroencephalography, Middle Aged, Surgery, Electrophysiology, Neuropsychology and Physiological Psychology, Behavioral data, Diffuse low-grade glioma, [ SCCO.NEUR ] Cognitive science/Neuroscience, Eeg rhythms, Female, medicine.symptom, Psychology, Eeg monitoring, 030217 neurology & neurosurgery
Abstract: International audience; Slow-growing, infiltrative brain tumours may modify the electrophysiological balance between the two hemispheres. To determine whether and how asymmetry of EEG rhythms during motor preparation might occur following " awake brain surgery " for this type of tumour, we recorded electroencephalograms during a simple visuo-manual reaction time paradigm performed by the patients between 3 and 12 months after surgery and compared them to a control group of 8 healthy subjects. Frequency analyses revealed imbalances between the injured and healthy hemispheres. More particularly, we observed a power increase in the δ frequency band near the lesion site and a power increase in the α and β frequency bands. Interestingly, these alterations seem to decrease for the two patients whose surgery were anterior to 9 months, independently of the size of the lesion. Reaction times did not reflect this pattern as they were clearly not inversely related to the anteriority of the surgery. Electrophysiology suggests here different processes of recovery compared to behavioral data and brings further insights for the understanding of EEG rhythms that should not be systematically confounded or assimilated with cognitive performances. EEG monitoring is rare for these patients, especially after awake brain surgery, however it is important.
Published: 2018

42. Constant versus periodic control under integral constraint on the input – applications to populations models

Author: Bayen, Térence, Rapaport, Alain, Tani, Fatima Zahra, Analyse, Calcul Scientifique Industriel et Optimisation de Montpellier (ACSIOM), Institut de Mathématiques et de Modélisation de Montpellier (I3M), Centre National de la Recherche Scientifique (CNRS)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM), Mathématiques, Informatique et STatistique pour l'Environnement et l'Agronomie (MISTEA), Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), ANR-16-CE04-0003,Thermomic,Un cadre thermodynamique pour la modélisation de la croissance et des dynamiques microbiennes(2016), ANR-10-LABX-0020,NUMEV,Digital and Hardware Solutions and Modeling for the Environement and Life Sciences(2010), Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA), ANR: 16-CE04-0003,THERMOMIC,Un cadre thermodynamique pour la modélisation de la croissance et des dynamiques microbiennes, ANR-10-LABX-0020/10-LABX-0020,NUMEV,Digital and Hardware Solutions and Modeling for the Environement and Life Sciences(2010), Institut Montpelliérain Alexander Grothendieck (IMAG), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Labex NUMEV, ANR THEROMIC, Rapaport, Alain, Un cadre thermodynamique pour la modélisation de la croissance et des dynamiques microbiennes - - Thermomic2016 - ANR-16-CE04-0003 - AAPG2016 - VALID, and Laboratoires d'excellence - Digital and Hardware Solutions and Modeling for the Environement and Life Sciences - - NUMEV2010 - ANR-10-LABX-0020 - LABX - VALID
Subjects: [MATH.MATH-OC] Mathematics [math]/Optimization and Control [math.OC], [MATH.MATH-OC]Mathematics [math]/Optimization and Control [math.OC]
Abstract: International audience; This presentation is about periodic optimal control problems governed by a system, linear w.r.t. the control u, under an integral constraint on u. In the one-dimensional setting, we give conditioon on the value of the cost function at steady state with a constant control \bar u can be improved by considering periodic controls u(.) with average value equal to \bar u. This leads to the so-called "over-yielding" met in several applications such as in resource-consumer models.With the use of the Pontryagin Maximum Principle, we provide the optimal synthesis of periodic strategies under the integral constraint. The results will be illustrated on a single population model in order to study the effect of periodic inputs on the utility of the stock of resource.
Published: 2018

43. Mining Frequent Subgraphs in Multigraphs

Author: Pascal Poncelet, Dino Ienco, Vijay Ingalalli, ADVanced Analytics for data SciencE (ADVANSE), Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Territoires, Environnement, Télédétection et Information Spatiale (UMR TETIS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-AgroParisTech-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Centre National de la Recherche Scientifique (CNRS), Labex NUMEV, ANR-10-LABX-0020,NUMEV,Digital and Hardware Solutions and Modeling for the Environement and Life Sciences(2010), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), and ANR-10-LABX-0020/10-LABX-0020,NUMEV,Digital and Hardware Solutions and Modeling for the Environement and Life Sciences(2010)
Subjects: Information Systems and Management, Theoretical computer science, Matching (graph theory), Computer science, Multigraphs, 02 engineering and technology, Frequent Subgraphs, Measure (mathematics), Theoretical Computer Science, Task (project management), [INFO.INFO-LG]Computer Science [cs]/Machine Learning [cs.LG], Artificial Intelligence, Simple (abstract algebra), 020204 information systems, 0202 electrical engineering, electronic engineering, information engineering, [INFO.INFO-DB]Computer Science [cs]/Databases [cs.DB], Multigraph, Graph, Computer Science Applications, Control and Systems Engineering, Graph (abstract data type), 020201 artificial intelligence & image processing, State (computer science), Software, Graph Mining, MathematicsofComputing_DISCRETEMATHEMATICS
Abstract: International audience; For more than a decade, extracting frequent patterns from single large graphs has been one of the research focuses. However, in this era of data eruption, rich and complex data is being generated at an unprecedented rate. This complex data can be represented as a multigraph structure-a generic and rich graph representation. In this paper, we propose a novel frequent subgraph mining approach MuGraM that can be applied to multigraphs. MuGraM is a generic frequent subgraph mining algorithm that discovers frequent multigraph patterns. MuGraM eciently performs the task of subgraph matching, which is crucial for support measure, and further leverages several optimization techniques for swift discovery of frequent subgraphs. Our experiments reveal two things: MuGraM discovers multigraph patterns, where other existing approaches are unable to do so; MuGraM, when applied to simple graphs, outperforms the state of the art approaches by at least one order of magnitude.
Published: 2018

44. Projet Étendard LabEx NUMEV GEM (Gene Expression Modeling)

Author: Palmeri, John, Laboratoire Charles Coulomb (L2C), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), and LabEx NUMEV
Subjects: [PHYS.PHYS.PHYS-BIO-PH]Physics [physics]/Physics [physics]/Biological Physics [physics.bio-ph], [PHYS.COND.CM-SM]Physics [physics]/Condensed Matter [cond-mat]/Statistical Mechanics [cond-mat.stat-mech], [PHYS.COND.CM-SCM]Physics [physics]/Condensed Matter [cond-mat]/Soft Condensed Matter [cond-mat.soft]
Abstract: National audience; Nous présentons les activités du Projet Étendard LabEx NUMEV GEM.
Published: 2018

45. Deciphering mRNA sequence determinants of protein production rate

Author: CIANDRINI, Luca, Laboratoire Charles Coulomb (L2C), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Joint Meeting GRISBI, Labex EpiGenMed, and Labex NUMEV
Subjects: [PHYS.PHYS.PHYS-BIO-PH]Physics [physics]/Physics [physics]/Biological Physics [physics.bio-ph], [PHYS.COND.CM-SM]Physics [physics]/Condensed Matter [cond-mat]/Statistical Mechanics [cond-mat.stat-mech], [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM]
Abstract: One of the greatest challenges in biophysical models of translation is to identify coding sequence features that affect the rate of translation and therefore the overall protein production in the cell. We propose an analytic method to solve a translation model based on the inhomogeneous totally asymmetric simple exclusion process, which allows us to unveil simple design principles of nucleotide sequences determining protein production rates. Our solution shows an excellent agreement when compared to numerical genome-wide simulations of S. cerevisiae transcript sequences and predicts that the first 10 codons, which is the ribosome footprint length on the mRNA, together with the value of the initiation rate, are the main determinants of protein production rate under physiological conditions. Finally, we interpret the obtained analytic results based on the evolutionary role of the codons’ choice for regulating translation rates and ribosome densities.
Published: 2018

46. First Results of Optimal Control of Average Biogas Production for the Chemostat Over an Infinite Horizon

Author: Antoine Haddon, Alain Rapaport, Héctor Ramírez, Mathématiques, Informatique et STatistique pour l'Environnement et l'Agronomie (MISTEA), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA), Departamento de Ingeniera Matematica [Santiago] (DIM), Universidad de Santiago de Chile [Santiago] (USACH), Departamento de Ingeniería Matemática [Santiago] (DIM), University of Chile [Santiago]-Centre National de la Recherche Scientifique (CNRS), IFAC, Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Universidad de Chile = University of Chile [Santiago] (UCHILE)-Centre National de la Recherche Scientifique (CNRS), CONICYT-Chile grant REDES : 150011, CONICYT-Chile under FONDECYT : 1160567, BASAL project (Centro de Modelamiento Matematico, Universidad de Chile), CONICYT-PFCHA/Doctorado Nacional : 2017-21170249, and LabEx NUMEV : AAP2017-2-08
Subjects: Large class, 0209 industrial biotechnology, Work (thermodynamics), Mathematical optimization, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, 0211 other engineering and technologies, Biomass, feedback, Biotechnologies, 02 engineering and technology, Chemostat, optimal control, infinite horizon, biogas production, chemostat, 020901 industrial engineering & automation, contrôle optimal, Optimization and Control, horizon infini, biogas, Optimisation et contrôle, Growth rate, Mathematics, Biogas production, 021103 operations research, biogaz, Optimal control, Control and Systems Engineering, Infinite horizon, [MATH.MATH-OC]Mathematics [math]/Optimization and Control [math.OC]
Abstract: International audience; In this work we study the optimal control problem of maximizing the average biogas production over an infnite horizon. We consider a large class of growth rate functions that depend on substrate and biomass concentrations and we solve this problem for the chemostat model. The obtained optimal control is a autonomous state feedback.
Published: 2018

47. Optimal periodic control of the chemostat with Contois growth function

Author: Alain Rapaport, Fatima Zahra Tani, Térence Bayen, Institut Montpelliérain Alexander Grothendieck (IMAG), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Mathématiques, Informatique et STatistique pour l'Environnement et l'Agronomie (MISTEA), Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), LabEx NUMEV incorporated into the I-Site MUSE (AAP2017- 2-08), French-Algerian AVERROES program of PhD 'bourses d'excellence', ANR-16-CE04-0003,Thermomic,Un cadre thermodynamique pour la modélisation de la croissance et des dynamiques microbiennes(2016), Mathématiques, Informatique et STatistique pour l'Environnement et l'Agronomie ( MISTEA ), Institut National de la Recherche Agronomique ( INRA ) -Institut national d’études supérieures agronomiques de Montpellier ( Montpellier SupAgro ), Institut Montpelliérain Alexander Grothendieck ( IMAG ), Université de Montpellier ( UM ) -Centre National de la Recherche Scientifique ( CNRS ), ANR : 16-CE04-0003,THERMOMIC,Un cadre thermodynamique pour la modélisation de la croissance et des dynamiques microbiennes, Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA), and ANR: 16-CE04-0003,THERMOMIC,Un cadre thermodynamique pour la modélisation de la croissance et des dynamiques microbiennes
Subjects: [ MATH.MATH-OC ] Mathematics [math]/Optimization and Control [math.OC], 0106 biological sciences, 0209 industrial biotechnology, Work (thermodynamics), fonction de croissance, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, 02 engineering and technology, Chemostat, 01 natural sciences, Pontryagin's minimum principle, Chemostat Model, 020901 industrial engineering & automation, contrôle optimal, Growth function, Optimization and Control, 010608 biotechnology, Applied mathematics, Over-yielding, Optimisation et contrôle, Pontryagin Maximum Principle, Mathematics, chemostat, [ SDV.BIO ] Life Sciences [q-bio]/Biotechnology, Optimal Periodic Control, Substrate concentration, Dilution, mathématiques appliquées, Constant rate, Control and Systems Engineering, chemostat model, optimal periodic control, pontryagin maximum principle, over-yielding, [MATH.MATH-OC]Mathematics [math]/Optimization and Control [math.OC]
Abstract: International audience; In this work, we examine the benefit of having periodic dilution rate in the chemostat model in terms of averaged conversion rate. We compare the effect of bringing a same substrate quantity by a periodic rate with a constant rate. We show that for the classical chemostat model with a Contois growth function, the performance of the averaged conversion rate can be improved under certain conditions. Using Pontryagin's Principle, we characterize the extremals of the problem which minimizes the averaged substrate concentration among periodic trajectories of a given period.
Published: 2018

48. Biophysical approach of the mucociliary function: Mucus rheology and beating coordination

Author: JORY, Myriam, Bellouma, Karim, Blanc, Christophe, Fort, Aurélie, Vernisse, Charlotte, CASANELLAS VILAGELIU, Laura, Vachier, Isabelle, Bourdin, Arnaud, MASSIERA, Gladys, Laboratoire Charles Coulomb (L2C), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Matière Molle, Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Physiologie & médecine expérimentale du Cœur et des Muscles [U 1046] (PhyMedExp), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Service d'allergologie et de pneumologie [Hôpital Arnaud de Villeneuve], Centre Hospitalier Universitaire de Montpellier (CHU Montpellier ), COST MP1305 Flowing Mater, Projet de thèseCollaboration avec le CHU de Montpellier, EPIGENMED and Labex NUMEV, and Projet de thèse: 'Approche biophysique de la fonction mucociliaire: rhéologie du mucus et coordination ciliaireCollaboration avec le CHU de Montpellier
Subjects: Micro-rheology, Optical Tweezers, [PHYS.PHYS.PHYS-BIO-PH]Physics [physics]/Physics [physics]/Biological Physics [physics.bio-ph], respiratory system, Mucus, Human bronchial epithelium, Image processing, Coordination, Micro rheology, Adhesion, Cilia, Rheology, Videomicroscopy, Macro Rheology
Abstract: National audience; The bronchial epithelium mucociliary function ensuring the lung continuous clearance relies on mucus rheological properties and cilia beating coordination. Our biophysical approach aims at understanding two points. First, the biochemical and physical parameters affecting the mucus viscoelastic properties and evaluating its use as a marker for the diagnosis of respiratory diseases. Secondly the cilia coordination and its coupling with the mucus.We performed rheological experiments on mucus extracted from Air Liquid Interface (ALI) cultures of bronchial epithelium reconstituted from bronchial biopsies. Our approach consists in combining standard macro-rheology to micro-rheology performed with optical tweezers, in order to quantify the mucus flowing behavior at different scales, from the cilia up to the mucus layer length scales.Macro- and micro-rheology give different results. At the macro-scale, we obtain an elastic plateau (1 to 2 Pa), a shear-thinning behaviour and a very low yield stress (0.05-0.2 Pa). While at the micro-scale, we obtain a viscous flow, with a very low viscoelastic modulus (10-3-10-2 Pa). Nevertheless, by applying local forces at the interfaces, we observe an important adhesion and elasticity. Mucus adhesion should be taken into account to understand the differences between these different length scales and more generally to characterize the mucus properties. We also perform original experiments using optical tweezers directly on the epithelium, to access the viscoelastic response in the various mucus layers. We obtain an increased elasticity in the vicinity to the epithelium. Moreover, comparison of physical properties of mucus from the culture and directly extracted from patient lungs, provides an additional validation of the ALI model.Finally, the specific methodology we developed to quantify cilia activity and coordination, allows us to map, the cilia spatial distribution, the beating frequency and orientation of each cilium, and their standard deviation within a cilia cluster (cell). Local quantification of the cilia activity coupled to the measurement of the mucus velocity field, should help to evaluate the efficiency of the mucociliary function and to understand the mechanisms of clearance.
Published: 2018

49. A conserved mechanism drives partition complex assembly on bacterial chromosomes and plasmids

Author: Debaugny, Roxanne, Sanchez, Aurore, Rech, Jérôme, Labourdette, Delphine, Dorignac, Jerome, Geniet, Frederic, Palmeri, John, Parmeggiani, Andrea, Boudsocq, François, LE BERRE, Véronique, Walter, Jean-Charles, Bouet, Jean-yves, Laboratoire de microbiologie et génétique moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés (LISBP), Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Charles Coulomb (L2C), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Dynamique des interactions membranaires normales et pathologiques (DIMNP), Université Montpellier 1 (UM1)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Systèmes Complexes et Phénomènes Nonlinéaires (SCPN), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), CNRS INPHYNITI program, Universite de Toulouse [APR14], Labex NUMEV [AAP 2013-2-005, 2015-2-055, 2016-1-024], ANR-14-CE09-0025,IBM,Visualisation et Modélisation de la Mitose Bactérienne(2014), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de la Recherche Agronomique (INRA), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Laboratoire de microbiologie et génétique moléculaires - UMR5100 (LMGM), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), and Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)
Subjects: [PHYS.PHYS.PHYS-BIO-PH]Physics [physics]/Physics [physics]/Biological Physics [physics.bio-ph], plasmid partition, DNA segregation, Article, Bacterial Proteins, Chromosome Segregation, Escherichia coli, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, ParABS, Vibrio cholerae, Quantitative Biology & Dynamical Systems, bactérie, Stochastic Processes, F plasmid, Systems Biology, adn, DNA Replication, Repair & Recombination, Articles, partitionnement, Chromosomes, Bacterial, Models, Theoretical, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Microbiology, Virology & Host Pathogen Interaction, Autre (Sciences du Vivant), Plasmids
Abstract: Synopsis Chromosome and plasmid segregation in bacteria are mostly driven by ParABS systems. These DNA partitioning machineries rely on large nucleoprotein complexes assembled on centromere sites (parS). However, the mechanism of how a few parS-bound ParB proteins nucleate the formation of highly concentrated ParB clusters remains unclear despite several proposed physico-mathematical models. We discriminated between these different models by varying some key parameters in vivo using the F plasmid partition system. We found that "Nucleation & caging" is the only coherent model recapitulating in vivo data. We also showed that the stochastic self-assembly of partition complexes (i) is a robust mechanism, (ii) does not directly involve ParA ATPase, (iii) results in a dynamic structure of discrete size independent of ParB concentration, and (iv) is not perturbed by active transcription but is by protein complexes. We refined the "Nucleation & caging" model and successfully applied it to the chromosomally encoded Par system of Vibrio cholerae, indicating that this stochastic self-assembly mechanism is widely conserved from plasmids to chromosomes.
Published: 2018

50. Étude et prédiction des interactions en coculture algale

Author: Krichen, Emna, ProdInra, Migration, Mathématiques, Informatique et STatistique pour l'Environnement et l'Agronomie (MISTEA), Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), MARine Biodiversity Exploitation and Conservation (UMR MARBEC), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Labex NUMEV, and ADEME
Subjects: [SDE.BE] Environmental Sciences/Biodiversity and Ecology, [MATH.MATH-DS]Mathematics [math]/Dynamical Systems [math.DS], systèmes dynamiques, [MATH.MATH-DS] Mathematics [math]/Dynamical Systems [math.DS], [INFO.INFO-MO] Computer Science [cs]/Modeling and Simulation, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, interactions, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, ComputingMilieux_MISCELLANEOUS, modélisation, micro-algues
Abstract: National audience
Published: 2018

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